Electron Microscopy Data Bank

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sample_name:"60S ribosomal protein L18a" AND citation_journal_name:"NATURE"

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EMD-16880

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60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native)

Release date: Feb. 21, 2024
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8ohd
Q-score: 0.531

DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wachalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR

Nature (2024) 627 pp. 445-452 [ DOI: doi:10.1038/s41586-024-07073-0 Pubmed: 38383785 ]

Sample:

60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
60s ribosomal subunit (Complex from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (Complex from Homo sapiens)
Ubiquitin-fold modifier 1 (9 kDa, Protein from Homo sapiens)
60s ribosomal subunit in complex with e3-ufm1 ligase (Complex)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
Cdk5 regulatory subunit-associated protein 3 (56 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
Ddrgk domain-containing protein 1 (35 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)

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EMD-16902

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60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)

Release date: Feb. 21, 2024
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8oj0
Q-score: 0.463

DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wachalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR

Nature (2024) 627 pp. 445-452 [ DOI: doi:10.1038/s41586-024-07073-0 Pubmed: 38383785 ]

Sample:

60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens environmental sample)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
60s ribosomal subunit bound to the e3-ufm1 complex and sec61 (Complex)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
60s ribosomal subunit (Complex from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (Complex from Homo sapiens)
Ubiquitin-fold modifier 1 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
Cdk5 regulatory subunit-associated protein 3 (56 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
Ddrgk domain-containing protein 1 (35 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)

[Show more]

EMD-16905

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60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)

Release date: Feb. 21, 2024
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8oj5
Q-score: 0.57

DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wachalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR

Nature (2024) 627 pp. 445-452 [ DOI: doi:10.1038/s41586-024-07073-0 Pubmed: 38383785 ]

Sample:

60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
E3-ufm1 complex bound to the 60s ribosome (Complex from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
Ubiquitin-fold modifier 1 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
Cdk5 regulatory subunit-associated protein 3 (56 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
Ddrgk domain-containing protein 1 (35 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)

[Show more]

EMD-16908

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60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)

Release date: Feb. 21, 2024
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8oj8
Q-score: 0.468

DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wachalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR

Nature (2024) 627 pp. 445-452 [ DOI: doi:10.1038/s41586-024-07073-0 Pubmed: 38383785 ]

Sample:

60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
60s ribosomal subunit (Complex from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
60s ribosomal subunit in complex with e3-ufm1 ligase, state 1 (Complex)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (Complex from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)

[Show more]

EMD-18382

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UFL1 E3 ligase bound 60S ribosome

Release date: Feb. 21, 2024
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8qfd
Q-score: 0.684

Makhlouf L, Peter JJ, Magnussen HM, Thakur R, Millrine D, Minshull TC, Harrison G, Varghese J, Lamoliatte F, Foglizzo M, Macartney T, Calabrese AN, Zeqiraj E, Kulathu Y

Nature (2024) 627 pp. 437-444 [ DOI: doi:10.1038/s41586-024-07093-w Pubmed: 38383789 ]

Sample:

28s rrna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
Ufm1 ribosome e3 ligase complex (Complex from Homo sapiens)
Ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
Large ribosomal subunit protein ul30 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
60s ribosome bound by the ufm1 ribosome e3 ligase complex. (Complex from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
60s ribosomal protein l10 (24 kDa, Protein from Homo sapiens)
E3 ufm1-protein ligase 1 (91 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)

[Show more]

EMD-16563

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80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex

Release date: Sept. 20, 2023
Resolution: 1.97 Å
EM Method: Single-particle
Fitted PDBs: 8ccs
Q-score: 0.64

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
Di-peptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
Elongating saccharomyces cerevisiae 80s ribosome in complex with ligands (Complex from Saccharomyces cerevisiae)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)

[Show more]

EMD-16591

Download Map 3D View

80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex

Release date: Sept. 20, 2023
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8cdl
Q-score: 0.533

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (13 kDa, Protein from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
Elongating saccharomyces cerevisiae 80s ribosome in complex with ligands (Complex from Saccharomyces cerevisiae)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
Dipeptide (296 Da, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)

[Show more]

EMD-16594

Download Map 3D View

Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Release date: Sept. 20, 2023
Resolution: 2.04 Å
EM Method: Single-particle
Fitted PDBs: 8cdr
Q-score: 0.615

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-diphosphate (443 Da, Ligand)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
80s saccharomyces cerevisiae ribosome in complex with eef2.sordarin and ligands (Complex from Saccharomyces cerevisiae)
[1r-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-o-methyl-beta-d-altropyranosyloxy)methyl]-4-formyl-4,4a,5,6,7,7a,8,8a-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-s-indacene-3a(1h)-carboxylic acid (494 Da, Ligand)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
Elongation factor 2 (93 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
Dipeptide (296 Da, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)

[Show more]

EMD-16609

Download Map 3D View

Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Release date: Sept. 20, 2023
Resolution: 2.05 Å
EM Method: Single-particle
Fitted PDBs: 8ceh
Q-score: 0.617

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41 (3 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-diphosphate (443 Da, Ligand)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
Rpl9a isoform 1 (21 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
80s saccharomyces cerevisiae ribosome in complex with eef2.sordarin and ligands (Complex from Saccharomyces cerevisiae)
[1r-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-o-methyl-beta-d-altropyranosyloxy)methyl]-4-formyl-4,4a,5,6,7,7a,8,8a-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-s-indacene-3a(1h)-carboxylic acid (494 Da, Ligand)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
Elongation factor 2 (93 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
Phosphate ion (94 Da, Ligand)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
Polypeptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)

[Show more]

EMD-16616

Download Map 3D View

Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Release date: Sept. 20, 2023
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 8cf5
Q-score: 0.548

Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G

Nature (2024) 625 pp. 393-400 [ Pubmed: 38030725 DOI: doi:10.1038/s41586-023-06780-4 ]

Sample:

Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna phe (24 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l41 (3 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
Hlj1_g0030400.mrna.1.cds.1 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
Rpl9a isoform 1 (21 kDa, Protein from Saccharomyces cerevisiae)
Water (18 Da, Ligand)
60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
Spermidine (145 Da, Ligand)
80s saccharomyces cerevisiae ribosome in complex with eef2.sordarin and ligands (Complex from Saccharomyces cerevisiae)
[1r-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-o-methyl-beta-d-altropyranosyloxy)methyl]-4-formyl-4,4a,5,6,7,7a,8,8a-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-s-indacene-3a(1h)-carboxylic acid (494 Da, Ligand)
Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
Elongation factor 2 (93 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s26 (13 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
Transfer rna fmet (24 kDa, RNA from Escherichia coli)
18s ribosomal rna (580 kDa, RNA from Saccharomyces cerevisiae)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
Polypeptide (296 Da, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-triphosphate (523 Da, Ligand)
40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s8-b (22 kDa, Protein from Saccharomyces cerevisiae)
Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
Messenger rna (12 kDa, RNA from Saccharomyces cerevisiae)
40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)

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