60S ribosomal subunit bound to the E3-UFM1 complex (native, UFM1 pulldown)
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 ]
60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native)
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 ]
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- Ubiquitin-fold modifier 1 (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- E3 ufm1-protein ligase 1 (Complex from Homo sapiens)
- 60s ribosomal subunit (Complex from Homo sapiens)
- 60s ribosomal subunit in complex with e3-ufm1 ligase (Complex)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- Cdk5 regulatory subunit-associated protein 3 (56 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- Ddrgk domain-containing protein 1 (35 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)
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 ]
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- Ubiquitin-fold modifier 1 (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- Ribosomal protein ul16-like (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)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- E3 ufm1-protein ligase 1 (Complex from Homo sapiens)
- 60s ribosomal subunit (Complex from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- Cdk5 regulatory subunit-associated protein 3 (56 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens environmental sample)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- Ddrgk domain-containing protein 1 (35 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal subunit bound to the e3-ufm1 complex and sec61 (Complex)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)
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 ]
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- Ubiquitin-fold modifier 1 (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- Cdk5 regulatory subunit-associated protein 3 (56 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- Ddrgk domain-containing protein 1 (35 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- E3-ufm1 complex bound to the 60s ribosome (Complex from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)
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 ]
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- Ribosomal protein ul16-like (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal subunit in complex with e3-ufm1 ligase, state 1 (Complex)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- E3 ufm1-protein ligase 1 (Complex from Homo sapiens)
- 60s ribosomal subunit (Complex from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- E3 ufm1-protein ligase 1 (89 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
Structure of P5A-ATPase Spf1, Apo form
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6xmp
Q-score: 0.475
McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E
Science (2020) 369 [ DOI: doi:10.1126/science.abc5809 Pubmed: 32973005 ]
- P5a-atpase spf1 apo form (Complex from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- P5a-type atpase (137 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of P5A-ATPase Spf1, AMP-PCP-bound form
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6xmq
Q-score: 0.466
McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E
Science (2020) 369 [ DOI: doi:10.1126/science.abc5809 Pubmed: 32973005 ]
- P5a-atpase spf1 amp-pcp-bound form (Complex from Saccharomyces cerevisiae)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- P5a-type atpase (137 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of P5A-ATPase Spf1, AlF4-bound form
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6xms
Q-score: 0.506
McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E
Science (2020) 369 [ DOI: doi:10.1126/science.abc5809 Pubmed: 32973005 ]
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- P5a-atpase spf1, alf4-bound form (Complex from Saccharomyces cerevisiae)
- P5a-type atpase (137 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of P5A-ATPase Spf1, BeF3-bound form
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6xmt
Q-score: 0.489
McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E
Science (2020) 369 [ DOI: doi:10.1126/science.abc5809 Pubmed: 32973005 ]
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- P5a-atpase spf1 bef3-bound form (Complex from Saccharomyces cerevisiae)
- P5a-type atpase (137 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of P5A-ATPase Spf1, endogenous substrate-bound
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6xmu
Q-score: 0.47
McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E
Science (2020) 369 [ DOI: doi:10.1126/science.abc5809 Pubmed: 32973005 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Putative endogenous substrate transmembrane helix (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- P5a-atpase spf1, endogenous substrate bound (Complex from Saccharomyces cerevisiae)
- P5a-type atpase (137 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))