Electron Microscopy Data Bank

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EMD-36331

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Atomic structure of wheat ribosome reveals unique features of the plant ribosomes

Release date: March 27, 2024
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8jiv
Q-score: 0.649

Mishra RK, Sharma P, Khaja FT, Uday AB, Hussain T

Structure (2024) 32 pp. 562- [ Pubmed: 38458197 DOI: doi:10.1016/j.str.2024.02.006 ]

Sample:

5s rrna (38 kDa, RNA from Triticum aestivum)
Ribosomal protein l18e/l15p domain-containing protein (21 kDa, Protein from Triticum aestivum)
Ribosomal protein l3 (44 kDa, Protein from Triticum aestivum)
Genome assembly, chromosome: ii (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein l36 (12 kDa, Protein from Triticum aestivum)
Ubiquitin-like domain-containing protein (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein l37a, expressed (10 kDa, Protein from Triticum aestivum)
Ribosomal protein l18e/l15p domain-containing protein (16 kDa, Protein from Triticum aestivum)
Ribosomal l28e/mak16 domain-containing protein (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein l13 (24 kDa, Protein from Triticum aestivum)
Ribosomal protein l13a (23 kDa, Protein from Triticum aestivum)
Ribosomal protein l6 alpha-beta domain-containing protein (21 kDa, Protein from Triticum aestivum)
Genome assembly, chromosome: ii (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein l21 (18 kDa, Protein from Triticum aestivum)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l7a (29 kDa, Protein from Triticum aestivum)
60s ribosomal protein l31 (14 kDa, Protein from Triticum aestivum)
Magnesium ion (24 Da, Ligand)
The large subunit of wheat ribosome (Complex from Triticum aestivum)
Ribosomal protein l7ae/l30e/s12e/gadd45 domain-containing protein (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein l29 (6 kDa, Protein from Triticum aestivum)
60s ribosomal protein l27 (15 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul22 (19 kDa, Protein from Triticum aestivum)
60s ribosomal protein l38 (8 kDa, Protein from Triticum aestivum)
5.8s rrna (50 kDa, RNA from Triticum aestivum)
60s ribosomal protein l34 (13 kDa, Protein from Triticum aestivum)
25s rrna (1 MDa, RNA from Triticum aestivum)
Ribosomal protein l5 eukaryotic c-terminal domain-containing protein (35 kDa, Protein from Triticum aestivum)
60s ribosomal protein l4 c-terminal domain-containing protein (44 kDa, Protein from Triticum aestivum)
60s ribosomal protein l35 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el32 (15 kDa, Protein from Triticum aestivum)
Ribosomal protein l19 (24 kDa, Protein from Triticum aestivum)
Kow domain-containing protein (14 kDa, Protein from Triticum aestivum)
Ribosomal protein l37 (10 kDa, Protein from Triticum aestivum)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l11 (20 kDa, Protein from Triticum aestivum)
Ribosomal protein l14e domain-containing protein (15 kDa, Protein from Triticum aestivum)
Genome assembly, chromosome: ii (14 kDa, Protein from Triticum aestivum)
Ribosomal protein l17 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul30 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein l18a (21 kDa, Protein from Triticum aestivum)
Trash domain-containing protein (18 kDa, Protein from Triticum aestivum)
60s ribosomal protein el33 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein l6 (25 kDa, Protein from Triticum aestivum)
Ribosomal protein l15 (24 kDa, Protein from Triticum aestivum)
Ribosomal protein l39 (6 kDa, Protein from Triticum aestivum)
Ribosomal protein l10e/l16 domain-containing protein (24 kDa, Protein from Triticum aestivum)
Ribosomal protein l2 c-terminal domain-containing protein (28 kDa, Protein from Triticum aestivum)

[Show more]

EMD-35634

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Wheat 80S ribosome stalled on AUG-Stop boron dependently

Release date: Feb. 21, 2024
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8ip8
Q-score: 0.579

Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T

Nat Chem Biol (2024) 20 pp. 605-614 [ Pubmed: 38267667 DOI: doi:10.1038/s41589-023-01513-0 ]

Sample:

40s ribosomal protein us19 (17 kDa, Protein from Triticum aestivum)
60s ribosomal rna (1 MDa, RNA from Triticum aestivum)
40s ribosomal protein us13 (17 kDa, Protein from Triticum aestivum)
60s ribosomal protein el20 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el41 (3 kDa, Protein from Oryza sativa)
40s ribosomal protein es7 (22 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul22 (19 kDa, Protein from Triticum aestivum)
60s ribosomal protein el42 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein el29 (6 kDa, Protein from Triticum aestivum)
40s ribosomal protein us12 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es28 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul30 (28 kDa, Protein from Triticum aestivum)
40s ribosomal protein el8 (29 kDa, Protein from Triticum aestivum)
60s ribosomal protein el28 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el30 (12 kDa, Protein from Triticum aestivum)
Trnai (24 kDa, RNA from Triticum aestivum)
40s ribosomal protein es27 (9 kDa, Protein from Triticum aestivum)
40s ribosomal protein es4 (30 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul29 (14 kDa, Protein from Triticum aestivum)
5.8s ribosomal rna (51 kDa, RNA from Triticum aestivum)
Rack1 (36 kDa, Protein from Triticum aestivum)
40s ribosomal protein us15 (17 kDa, Protein from Triticum aestivum)
5s ribosomal rna (38 kDa, RNA from Triticum aestivum)
40s ribosomal protein es17 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein es30 (6 kDa, Protein from Triticum aestivum)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein el6 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el24 (18 kDa, Protein from Triticum aestivum)
40s ribosomal protein us11 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el15 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el14 (15 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul14 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es8 (25 kDa, Protein from Triticum aestivum)
60s ribosomal protein el43 (10 kDa, Protein from Triticum aestivum)
Mrna (2 kDa, RNA from Triticum aestivum)
60s ribosomal protein ul3 (44 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul23 (16 kDa, Protein from Triticum aestivum)
Cca end of e-trna (894 Da, RNA from Triticum aestivum)
60s ribosomal protein el27 (15 kDa, Protein from Triticum aestivum)
Eukaryotic release factor 1 (49 kDa, Protein from Triticum aestivum)
40s ribosomal protein es10 (20 kDa, Protein from Triticum aestivum)
40s ribosomal protein us14 (6 kDa, Protein from Triticum aestivum)
60s ribosomal protein el22 (14 kDa, Protein from Triticum aestivum)
40s ribosomal protein us8 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el36 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul13 (23 kDa, Protein from Triticum aestivum)
40s ribosomal protein us17 (17 kDa, Protein from Triticum aestivum)
40s ribosomal protein us5 (29 kDa, Protein from Triticum aestivum)
18s ribosomal rna (583 kDa, RNA from Triticum aestivum)
40s ribosomal protein us7 (22 kDa, Protein from Triticum aestivum)
40s ribosomal protein es1 (30 kDa, Protein from Triticum aestivum)
60s ribosomal protein el21 (18 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul16 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul2 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul5 (20 kDa, Protein from Triticum aestivum)
40s ribosomal protein es6 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul4 (44 kDa, Protein from Triticum aestivum)
40s ribosomal protein es24 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein us4 (22 kDa, Protein from Triticum aestivum)
40s ribosomal protein us10 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el18 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el32 (15 kDa, Protein from Triticum aestivum)
Zinc ion (65 Da, Ligand)
60s ribosomal protein el31 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul18 (34 kDa, Protein from Triticum aestivum)
40s ribosomal protein es19 (17 kDa, Protein from Triticum aestivum)
40s ribosomal protein us2 (33 kDa, Protein from Triticum aestivum)
Wheat 80s ribosome stalled on aug-stop boron dependently (Complex from Triticum aestivum)
60s ribosomal protein el34 (13 kDa, Protein from Triticum aestivum)
40s ribosomal protein us9 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el37 (10 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul6 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el13 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el33 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein el19 (24 kDa, Protein from Triticum aestivum)
40s ribosomal protein es26 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein us3 (25 kDa, Protein from Triticum aestivum)
60s ribosomal protein el40 (14 kDa, Protein from Triticum aestivum)
40s ribosomal protein es21 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein el39 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein el38 (8 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul15 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein es25 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul24 (17 kDa, Protein from Triticum aestivum)

[Show more]

EMD-35637

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Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide

Release date: Feb. 21, 2024
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ipa
Q-score: 0.471

Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T

Nat Chem Biol (2024) 20 pp. 605-614 [ Pubmed: 38267667 DOI: doi:10.1038/s41589-023-01513-0 ]

Sample:

40s ribosomal protein us19 (17 kDa, Protein from Triticum aestivum)
60s ribosomal rna (1 MDa, RNA from Triticum aestivum)
40s ribosomal protein us13 (17 kDa, Protein from Triticum aestivum)
60s ribosomal protein el20 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el41 (3 kDa, Protein from Oryza sativa)
40s ribosomal protein es7 (22 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul22 (19 kDa, Protein from Triticum aestivum)
60s ribosomal protein el42 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein el29 (6 kDa, Protein from Triticum aestivum)
40s ribosomal protein us12 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es28 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul30 (28 kDa, Protein from Triticum aestivum)
40s ribosomal protein el8 (29 kDa, Protein from Triticum aestivum)
60s ribosomal protein el28 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el30 (12 kDa, Protein from Triticum aestivum)
Trnai (24 kDa, RNA from Triticum aestivum)
40s ribosomal protein es27 (9 kDa, Protein from Triticum aestivum)
40s ribosomal protein es4 (30 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul29 (14 kDa, Protein from Triticum aestivum)
5.8s ribosomal rna (51 kDa, RNA from Triticum aestivum)
Rack1 (36 kDa, Protein from Triticum aestivum)
40s ribosomal protein us15 (17 kDa, Protein from Triticum aestivum)
5s ribosomal rna (38 kDa, RNA from Triticum aestivum)
40s ribosomal protein es17 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein es30 (6 kDa, Protein from Triticum aestivum)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein el6 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el24 (18 kDa, Protein from Triticum aestivum)
40s ribosomal protein us11 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el15 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el14 (15 kDa, Protein from Triticum aestivum)
Wheat 80s ribosome stalled on aug-stop boron dependently with cycloheximide (Complex from Triticum aestivum)
60s ribosomal protein ul14 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es8 (25 kDa, Protein from Triticum aestivum)
60s ribosomal protein el43 (10 kDa, Protein from Triticum aestivum)
Mrna (2 kDa, RNA from Triticum aestivum)
60s ribosomal protein ul3 (44 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul23 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el27 (15 kDa, Protein from Triticum aestivum)
Eukaryotic release factor 1 (49 kDa, Protein from Triticum aestivum)
40s ribosomal protein es10 (20 kDa, Protein from Triticum aestivum)
40s ribosomal protein us14 (6 kDa, Protein from Triticum aestivum)
60s ribosomal protein el22 (14 kDa, Protein from Triticum aestivum)
40s ribosomal protein us8 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el36 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul13 (23 kDa, Protein from Triticum aestivum)
40s ribosomal protein us17 (17 kDa, Protein from Triticum aestivum)
40s ribosomal protein us5 (29 kDa, Protein from Triticum aestivum)
18s ribosomal rna (583 kDa, RNA from Triticum aestivum)
40s ribosomal protein us7 (22 kDa, Protein from Triticum aestivum)
40s ribosomal protein es1 (30 kDa, Protein from Triticum aestivum)
60s ribosomal protein el21 (18 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul16 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul2 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul5 (20 kDa, Protein from Triticum aestivum)
40s ribosomal protein es6 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul4 (44 kDa, Protein from Triticum aestivum)
40s ribosomal protein es24 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein us4 (22 kDa, Protein from Triticum aestivum)
40s ribosomal protein us10 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el18 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el32 (15 kDa, Protein from Triticum aestivum)
Zinc ion (65 Da, Ligand)
60s ribosomal protein el31 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul18 (34 kDa, Protein from Triticum aestivum)
40s ribosomal protein es19 (17 kDa, Protein from Triticum aestivum)
40s ribosomal protein us2 (33 kDa, Protein from Triticum aestivum)
60s ribosomal protein el34 (13 kDa, Protein from Triticum aestivum)
40s ribosomal protein us9 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el37 (10 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul6 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el13 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el33 (12 kDa, Protein from Triticum aestivum)
4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
60s ribosomal protein el19 (24 kDa, Protein from Triticum aestivum)
40s ribosomal protein es26 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein us3 (25 kDa, Protein from Triticum aestivum)
60s ribosomal protein el40 (14 kDa, Protein from Triticum aestivum)
40s ribosomal protein es21 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein el39 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein el38 (8 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul15 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein es25 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul24 (17 kDa, Protein from Triticum aestivum)

[Show more]

EMD-35638

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Wheat 80S ribosome pausing on AUG-Stop with cycloheximide

Release date: Feb. 21, 2024
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ipb
Q-score: 0.466

Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T

Nat Chem Biol (2024) 20 pp. 605-614 [ Pubmed: 38267667 DOI: doi:10.1038/s41589-023-01513-0 ]

Sample:

40s ribosomal protein us19 (17 kDa, Protein from Triticum aestivum)
60s ribosomal rna (1 MDa, RNA from Triticum aestivum)
40s ribosomal protein us13 (17 kDa, Protein from Triticum aestivum)
60s ribosomal protein el20 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el41 (3 kDa, Protein from Oryza sativa)
40s ribosomal protein es7 (22 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul22 (19 kDa, Protein from Triticum aestivum)
60s ribosomal protein el42 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein el29 (6 kDa, Protein from Triticum aestivum)
40s ribosomal protein us12 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es28 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul30 (28 kDa, Protein from Triticum aestivum)
40s ribosomal protein el8 (29 kDa, Protein from Triticum aestivum)
60s ribosomal protein el28 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el30 (12 kDa, Protein from Triticum aestivum)
Trnai (24 kDa, RNA from Triticum aestivum)
40s ribosomal protein es27 (9 kDa, Protein from Triticum aestivum)
40s ribosomal protein es4 (30 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul29 (14 kDa, Protein from Triticum aestivum)
5.8s ribosomal rna (51 kDa, RNA from Triticum aestivum)
Rack1 (36 kDa, Protein from Triticum aestivum)
40s ribosomal protein us15 (17 kDa, Protein from Triticum aestivum)
5s ribosomal rna (38 kDa, RNA from Triticum aestivum)
40s ribosomal protein es17 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein es30 (6 kDa, Protein from Triticum aestivum)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein el6 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el24 (18 kDa, Protein from Triticum aestivum)
40s ribosomal protein us11 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el15 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el14 (15 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul14 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es8 (25 kDa, Protein from Triticum aestivum)
60s ribosomal protein el43 (10 kDa, Protein from Triticum aestivum)
Mrna (2 kDa, RNA from Triticum aestivum)
60s ribosomal protein ul3 (44 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul23 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el27 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein es10 (20 kDa, Protein from Triticum aestivum)
40s ribosomal protein us14 (6 kDa, Protein from Triticum aestivum)
60s ribosomal protein el22 (14 kDa, Protein from Triticum aestivum)
40s ribosomal protein us8 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el36 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul13 (23 kDa, Protein from Triticum aestivum)
40s ribosomal protein us17 (17 kDa, Protein from Triticum aestivum)
40s ribosomal protein us5 (29 kDa, Protein from Triticum aestivum)
18s ribosomal rna (583 kDa, RNA from Triticum aestivum)
40s ribosomal protein us7 (22 kDa, Protein from Triticum aestivum)
40s ribosomal protein es1 (30 kDa, Protein from Triticum aestivum)
60s ribosomal protein el21 (18 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul16 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul2 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul5 (20 kDa, Protein from Triticum aestivum)
40s ribosomal protein es6 (28 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul4 (44 kDa, Protein from Triticum aestivum)
40s ribosomal protein es24 (15 kDa, Protein from Triticum aestivum)
40s ribosomal protein us4 (22 kDa, Protein from Triticum aestivum)
40s ribosomal protein us10 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein el18 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el32 (15 kDa, Protein from Triticum aestivum)
Zinc ion (65 Da, Ligand)
Wheat 80s ribosome pausing on aug-stop with cycloheximide (Complex from Triticum aestivum)
60s ribosomal protein el31 (14 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul18 (34 kDa, Protein from Triticum aestivum)
40s ribosomal protein es19 (17 kDa, Protein from Triticum aestivum)
40s ribosomal protein us2 (33 kDa, Protein from Triticum aestivum)
60s ribosomal protein el34 (13 kDa, Protein from Triticum aestivum)
40s ribosomal protein us9 (16 kDa, Protein from Triticum aestivum)
60s ribosomal protein el37 (10 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul6 (21 kDa, Protein from Triticum aestivum)
60s ribosomal protein el13 (24 kDa, Protein from Triticum aestivum)
60s ribosomal protein el33 (12 kDa, Protein from Triticum aestivum)
4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
60s ribosomal protein el19 (24 kDa, Protein from Triticum aestivum)
40s ribosomal protein es26 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein us3 (25 kDa, Protein from Triticum aestivum)
60s ribosomal protein el40 (14 kDa, Protein from Triticum aestivum)
40s ribosomal protein es21 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein el39 (9 kDa, Protein from Triticum aestivum)
60s ribosomal protein el38 (8 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul15 (16 kDa, Protein from Triticum aestivum)
40s ribosomal protein es25 (12 kDa, Protein from Triticum aestivum)
60s ribosomal protein ul24 (17 kDa, Protein from Triticum aestivum)

[Show more]

EMD-29407

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60S subunit of the Giardia lamblia 80S ribosome

Release date: Jan. 31, 2024
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8fru
Q-score: 0.648

Eiler DR, Wimberly BT, Bilodeau DY, Taliaferro JM, Reigan P, Rissland OS, Kieft JS

Structure (2024) 32 pp. 400- [ DOI: doi:10.1016/j.str.2023.12.015 Pubmed: 38242118 ]

Sample:

60s ribosomal protein el33 (13 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul23 (16 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el19 (23 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul18 (33 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul24 (15 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el41 (2 kDa, Protein from Giardia intestinalis assemblage A)
Spermidine (145 Da, Ligand)
60s ribosomal protein ul22 (18 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el36 (10 kDa, Protein from Giardia intestinalis assemblage A)
Sodium ion (22 Da, Ligand)
Water (18 Da, Ligand)
60s ribosomal protein el24 (12 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el30 (11 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul5 (19 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul29 (14 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el42 (12 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul13 (22 kDa, Protein from Giardia intestinalis assemblage A)
Potassium ion (39 Da, Ligand)
60s ribosomal subunit of the 80s giardia intestinalis assemblage a ribosome (Complex from Giardia intestinalis assemblage A)
60s ribosomal protein el39 (6 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul15 (17 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el38 (8 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el37 (11 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el18 (20 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el20 (24 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul3 (42 kDa, Protein from Giardia intestinalis assemblage A)
5s rrna (38 kDa, RNA from Giardia intestinalis assemblage A)
60s ribosomal protein el22 (19 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el31 (12 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el40 (14 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el14 (14 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el21 (18 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul14 (15 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul30 (27 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el32 (15 kDa, Protein from Giardia intestinalis assemblage A)
28s rrna (871 kDa, RNA from Giardia intestinalis assemblage A)
60s ribosomal protein el15 (24 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el8 (25 kDa, Protein from Giardia intestinalis assemblage A)
Zinc ion (65 Da, Ligand)
5.8s rrna (45 kDa, RNA from Giardia intestinalis assemblage A)
60s ribosomal protein el27 (15 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el34 (13 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el13 (26 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el43 (10 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul6 (20 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul4 (35 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein el29 (7 kDa, Protein from Giardia intestinalis assemblage A)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein ul16 (24 kDa, Protein from Giardia intestinalis assemblage A)
60s ribosomal protein ul2 (27 kDa, Protein from Giardia intestinalis assemblage A)

[Show more]

EMD-40344

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Terminating ribosome with SRI-41315

Release date: Dec. 27, 2023
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8scb
Q-score: 0.589

Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S

To Be Published

Sample:

Atp binding cassette subfamily e member 1 (67 kDa, Protein from Oryctolagus cuniculus)
Receptor for activated c kinase 1 (rack1) (35 kDa, Protein from Oryctolagus cuniculus)
El33 (12 kDa, Protein from Oryctolagus cuniculus)
Ubiquitin a-52 residue ribosomal protein fusion product 1 (10 kDa, Protein from Oryctolagus cuniculus)
Es27 (9 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
Es31 (18 kDa, Protein from Oryctolagus cuniculus)
Terminating rabbit ribosome (4 MDa, Complex from Oryctolagus cuniculus)
60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
E_trna (24 kDa, RNA from Oryctolagus cuniculus)
Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
Es21 (9 kDa, Protein from Oryctolagus cuniculus)
Us4 (22 kDa, Protein from Oryctolagus cuniculus)
Iron/sulfur cluster (351 Da, Ligand)
Es8 (24 kDa, Protein from Oryctolagus cuniculus)
Us14 (6 kDa, Protein from Oryctolagus cuniculus)
Us5 (31 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic peptide chain release factor subunit 1 (51 kDa, Protein from Homo sapiens)
El22 (14 kDa, Protein from Oryctolagus cuniculus)
Us9 (16 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
Ul24 (17 kDa, Protein from Oryctolagus cuniculus)
El13 (24 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
Es7 (22 kDa, Protein from Oryctolagus cuniculus)
Es6 (28 kDa, Protein from Oryctolagus cuniculus)
Water (18 Da, Ligand)
60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
5.8s_rrna (50 kDa, RNA from Oryctolagus cuniculus)
S10_plectin domain-containing protein (18 kDa, Protein from Oryctolagus cuniculus)
Us19 (17 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
Ul13 (23 kDa, Protein from Oryctolagus cuniculus)
Es25 (13 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein s3 (26 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s26 (13 kDa, Protein from Oryctolagus cuniculus)
El41 (3 kDa, Protein from Oryctolagus cuniculus)
El30 (12 kDa, Protein from Oryctolagus cuniculus)
El42 (12 kDa, Protein from Oryctolagus cuniculus)
Es28 (7 kDa, Protein from Oryctolagus cuniculus)
Us15 (17 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
Us10 (13 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
Us13 (17 kDa, Protein from Oryctolagus cuniculus)
Nc (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
Us11 (18 kDa, Protein from Oryctolagus cuniculus)
El35 (14 kDa, Protein from Oryctolagus cuniculus)
Us2 (sa) (32 kDa, Protein from Oryctolagus cuniculus)
5s_rrna (38 kDa, RNA from Oryctolagus cuniculus)
Ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
18s_rrna (603 kDa, RNA from Oryctolagus cuniculus)
Zinc ion (65 Da, Ligand)
Mrna (63 kDa, RNA from Homo sapiens)
(2s,4as)-2-cyclobutyl-10-methyl-3-phenyl-2,10-dihydropyrimido[4,5-b]quinoline-4,5(3h,4ah)-dione (359 Da, Ligand)
Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
Es12 (14 kDa, Protein from Oryctolagus cuniculus)
El39 (6 kDa, Protein from Oryctolagus cuniculus)
Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
Es1 (30 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
El31 (14 kDa, Protein from Oryctolagus cuniculus)
El43 (10 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
Es17 (15 kDa, Protein from Oryctolagus cuniculus)
Us8 (14 kDa, Protein from Oryctolagus cuniculus)
El32 (15 kDa, Protein from Oryctolagus cuniculus)
28s_rrna (1 MDa, RNA from Oryctolagus cuniculus)
Us12 (15 kDa, Protein from Oryctolagus cuniculus)
El21 (18 kDa, Protein from Oryctolagus cuniculus)
60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
El20 (20 kDa, Protein from Oryctolagus cuniculus)
Us7 (22 kDa, Protein from Oryctolagus cuniculus)
P_trna (24 kDa, RNA from Oryctolagus cuniculus)
Es19 (16 kDa, Protein from Oryctolagus cuniculus)
El23 (17 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
Es30 (14 kDa, Protein from Oryctolagus cuniculus)
Us17 (18 kDa, Protein from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
Es4 (s4 x isoform) (29 kDa, Protein from Oryctolagus cuniculus)
El28 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)

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EMD-15806

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Cryo-EM structure of the plant 80S ribosome

Release date: Aug. 23, 2023
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8b2l
Q-score: 0.639

Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R

Nat Plants (2023) 9 pp. 987-1000 [ DOI: doi:10.1038/s41477-023-01407-y Pubmed: 37156858 ]

Sample:

Spermine (202 Da, Ligand)
El36 (60s ribosomal protein l36) (12 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s4 (29 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s27 (9 kDa, Protein from Nicotiana tabacum)
Ul2 (60s ribosomal protein l8) (28 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein sa (35 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l44 (12 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s23 (15 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l30-like (12 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l32-1 (15 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s3a (29 kDa, Protein from Nicotiana tabacum)
Ul3 (60s ribosomal protein l3) (44 kDa, Protein from Nicotiana tabacum)
Ribosomal protein l19 (25 kDa, Protein from Nicotiana tabacum)
Trna (24 kDa, RNA from Nicotiana tabacum)
40s ribosomal protein s30 (6 kDa, Protein from Nicotiana tabacum)
18s rrna (583 kDa, RNA from Nicotiana tabacum)
50s ribosomal protein l22, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l29 (7 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l23 (15 kDa, Protein from Nicotiana tabacum)
Spermidine (145 Da, Ligand)
60s ribosomal protein l34 (13 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l7a (29 kDa, Protein from Nicotiana tabacum)
Water (18 Da, Ligand)
60s ribosomal protein l22-2-like (14 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s21 (9 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s7 (22 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s11-like (17 kDa, Protein from Nicotiana tabacum)
Ul6 (60s ribosomal protein l9) (22 kDa, Protein from Nicotiana tabacum)
5.8s rrna (52 kDa, RNA from Nicotiana tabacum)
El28 (60s ribosomal protein l28) (15 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l37a (10 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l21-1-like (18 kDa, Protein from Nicotiana tabacum)
40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
40s ribosomal protein s8 (25 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l38 (8 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s28 (7 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s15a-1 (14 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l13 (23 kDa, Protein from Nicotiana tabacum)
Ubiquitin-40s ribosomal protein s27a-like (17 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s15-like (17 kDa, Protein from Nicotiana tabacum)
Ul24 (60s ribosomal protein l26) (16 kDa, Protein from Nicotiana tabacum)
30s ribosomal protein s15, chloroplastic (17 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s9-2-like (23 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l41 (3 kDa, Protein from Nicotiana tabacum)
Ribosomal protein l37 (10 kDa, Protein from Nicotiana tabacum)
5s rrna (38 kDa, RNA from Nicotiana tabacum)
40s ribosomal protein s12 (15 kDa, Protein from Nicotiana tabacum)
Mrna (3 kDa, RNA from Nicotiana tabacum)
60s ribosomal protein l18-2-like (20 kDa, Protein from Nicotiana tabacum)
Guanine nucleotide-binding protein subunit beta-like protein (36 kDa, Protein from Nicotiana tabacum)
Potassium ion (39 Da, Ligand)
40s ribosomal protein s20-2 (13 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l23a (17 kDa, Protein from Nicotiana tabacum)
Ribosomal protein l15 (24 kDa, Protein from Nicotiana tabacum)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s29 (6 kDa, Protein from Nicotiana tabacum)
El31 (60s ribosomal protein l31) (13 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s3-2-like (27 kDa, Protein from Nicotiana tabacum)
Zinc ion (65 Da, Ligand)
40s ribosomal protein s10-1-like (23 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s16 (16 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l14-1 (15 kDa, Protein from Nicotiana tabacum)
Ul15 (60s ribosomal protein l27a) (16 kDa, Protein from Nicotiana tabacum)
Ul13 (60s ribosomal protein l13a) (23 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l39-3 (6 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l35-like (14 kDa, Protein from Nicotiana tabacum)
El27 (60s ribosomal protein l27) (15 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s6 (28 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s26 (14 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s24 (15 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s25 (11 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l5-like (34 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l18a (21 kDa, Protein from Nicotiana tabacum)
25s rrna (1 MDa, RNA from Nicotiana tabacum)
40s ribosomal protein s2-3-like (30 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s18 (17 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s14-2 (16 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s17-like (16 kDa, Protein from Nicotiana tabacum)
Ul5 (60s ribosomal protein l11) (20 kDa, Protein from Nicotiana tabacum)
Ul16 (60s ribosomal protein l10) (25 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l24-like (18 kDa, Protein from Nicotiana tabacum)
Ul4 (60s ribosomal protein l4) (44 kDa, Protein from Nicotiana tabacum)
60s ribosomal protein l7-4-like (28 kDa, Protein from Nicotiana tabacum)
Nascent chain (2 kDa, Protein from Nicotiana tabacum)
El33 (60s ribosomal protein l35a) (12 kDa, Protein from Nicotiana tabacum)
El6 (60s ribosomal protein l6) (25 kDa, Protein from Nicotiana tabacum)
Magnesium ion (24 Da, Ligand)
40s ribosomal protein s19-3 (16 kDa, Protein from Nicotiana tabacum)
40s ribosomal protein s5-like (23 kDa, Protein from Nicotiana tabacum)

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EMD-15773

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Cryo-EM structure of the plant 60S subunit

Release date: June 7, 2023
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 8azw
Q-score: 0.675

Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R

Nat Plants (2023) 9 pp. 987-1000 [ DOI: doi:10.1038/s41477-023-01407-y Pubmed: 37156858 ]

Sample:

Ul4 (60s ribosomal protein l4) (44 kDa, Protein from common tobacco)
Spermidine (145 Da, Ligand)
Spermine (202 Da, Ligand)
El27 (60s ribosomal protein l27) (15 kDa, Protein from common tobacco)
Water (18 Da, Ligand)
El19 (60s ribosomal protein l19) (25 kDa, Protein from common tobacco)
Ul30 (60s ribosomal protein l7) (28 kDa, Protein from common tobacco)
Nascent chain (2 kDa, Protein from common tobacco)
5.8s rrna (52 kDa, RNA from common tobacco)
El37 (60s ribosomal protein l37) (10 kDa, Protein from common tobacco)
El39 (60s ribosomal protein l39) (6 kDa, Protein from common tobacco)
Ul5 (60s ribosomal protein l11) (20 kDa, Protein from common tobacco)
El33 (60s ribosomal protein l35a) (12 kDa, Protein from common tobacco)
El15 (60s ribosomal protein l15) (24 kDa, Protein from common tobacco)
El18 (60s ribosomal protein l18) (20 kDa, Protein from common tobacco)
Ul29 (60s ribosomal protein l35) (14 kDa, Protein from common tobacco)
El22 (60s ribosomal protein l22) (14 kDa, Protein from common tobacco)
El42 (60s ribosomal protein l42) (12 kDa, Protein from common tobacco)
El32 (60s ribosomal protein l32) (15 kDa, Protein from common tobacco)
El40 (60s ribosomal protein l40) (14 kDa, Protein from common tobacco)
Potassium ion (39 Da, Ligand)
25s rrna (1 MDa, RNA from common tobacco)
Ul13 (60s ribosomal protein l13a) (23 kDa, Protein from common tobacco)
El21 (60s ribosomal protein l21) (18 kDa, Protein from common tobacco)
Ul15 (60s ribosomal protein l27a) (16 kDa, Protein from common tobacco)
El13 (60s ribosomal protein l13) (23 kDa, Protein from common tobacco)
El36 (60s ribosomal protein l36) (12 kDa, Protein from common tobacco)
El14 (60s ribosomal protein l14) (15 kDa, Protein from common tobacco)
El28 (60s ribosomal protein l28) (15 kDa, Protein from common tobacco)
5s rrna (38 kDa, RNA from common tobacco)
El34 (60s ribosomal protein l34) (13 kDa, Protein from common tobacco)
40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
El6 (60s ribosomal protein l6) (25 kDa, Protein from common tobacco)
Ul3 (60s ribosomal protein l3) (44 kDa, Protein from common tobacco)
El31 (60s ribosomal protein l31) (13 kDa, Protein from common tobacco)
El38 (60s ribosomal protein l38) (8 kDa, Protein from common tobacco)
Ul23 (60s ribosomal protein l23a) (17 kDa, Protein from common tobacco)
El30 (60s ribosomal protein l30) (12 kDa, Protein from common tobacco)
El41 (60s ribosomal protein l41) (3 kDa, Protein from common tobacco)
Zinc ion (65 Da, Ligand)
El20 (60s ribosomal protein l18a) (21 kDa, Protein from common tobacco)
Ul6 (60s ribosomal protein l9) (22 kDa, Protein from common tobacco)
El43 (60s ribosomal protein l37a) (10 kDa, Protein from common tobacco)
El8 (60s ribosomal protein l7a) (29 kDa, Protein from common tobacco)
Ul18 (60s ribosomal protein l5) (34 kDa, Protein from common tobacco)
El29 (60s ribosomal protein l29) (7 kDa, Protein from common tobacco)
Ul14 (60s ribosomal protein l23) (15 kDa, Protein from common tobacco)
Ul2 (60s ribosomal protein l8) (28 kDa, Protein from common tobacco)
El24 (60s ribosomal protein l24) (18 kDa, Protein from common tobacco)
Ul16 (60s ribosomal protein l10) (25 kDa, Protein from common tobacco)
Ul24 (60s ribosomal protein l26) (16 kDa, Protein from common tobacco)
Magnesium ion (24 Da, Ligand)
Ul22 (60s ribosomal protein l17) (20 kDa, Protein from common tobacco)

[Show more]

EMD-29759

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mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)

Release date: April 19, 2023
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 8g60
Q-score: 0.576

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ DOI: doi:10.1038/s41586-023-05908-w Pubmed: 37020024 ]

Sample:

El13 (31 kDa, Protein from Homo sapiens)
Us2 (32 kDa, Protein from Homo sapiens)
Us4 (22 kDa, Protein from Homo sapiens)
Us14 (6 kDa, Protein from Homo sapiens)
Us19 (17 kDa, Protein from Homo sapiens)
El40 (14 kDa, Protein from Homo sapiens)
El34 (13 kDa, Protein from Homo sapiens)
El19 (23 kDa, Protein from Homo sapiens)
Es24 (15 kDa, Protein from Homo sapiens)
Es7 (22 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
Mrna (19 kDa, RNA from Homo sapiens)
Us8 (14 kDa, Protein from Homo sapiens)
Ul10 (34 kDa, Protein from Homo sapiens)
El18 (21 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
Ul3 (46 kDa, Protein from Homo sapiens)
Ul22 (21 kDa, Protein from Homo sapiens)
Phenylalanine (165 Da, Ligand)
El41 (3 kDa, Protein from Homo sapiens)
Es30 (14 kDa, Protein from Homo sapiens)
Us9 (16 kDa, Protein from Homo sapiens)
Rack1 (35 kDa, Protein from Homo sapiens)
Anisomycin (265 Da, Ligand)
Spermidine (145 Da, Ligand)
Es27 (9 kDa, Protein from Homo sapiens)
Ul6 (21 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
Us3 (26 kDa, Protein from Homo sapiens)
Ul2 (28 kDa, Protein from Homo sapiens)
Ul29 (14 kDa, Protein from Homo sapiens)
Ul16 (24 kDa, Protein from Homo sapiens)
El37 (11 kDa, Protein from Homo sapiens)
Es21 (9 kDa, Protein from Homo sapiens)
Ul24 (17 kDa, Protein from Homo sapiens)
Ul18 (34 kDa, Protein from Homo sapiens)
Ul30 (29 kDa, Protein from Homo sapiens)
El42 (12 kDa, Protein from Homo sapiens)
Es10 (18 kDa, Protein from Homo sapiens)
Us5 (31 kDa, Protein from Homo sapiens)
A-site trna (24 kDa, RNA from Homo sapiens)
Es6 (28 kDa, Protein from Homo sapiens)
Ul5 (20 kDa, Protein from Homo sapiens)
Us17 (18 kDa, Protein from Homo sapiens)
Us11 (16 kDa, Protein from Homo sapiens)
Es8 (24 kDa, Protein from Homo sapiens)
Es28 (7 kDa, Protein from Homo sapiens)
Ul23 (17 kDa, Protein from Homo sapiens)
El33 (12 kDa, Protein from Homo sapiens)
El27 (15 kDa, Protein from Homo sapiens)
El28 (15 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
Ul4 (47 kDa, Protein from Homo sapiens)
Us7 (22 kDa, Protein from Homo sapiens)
Es1 (30 kDa, Protein from Homo sapiens)
Methionine (149 Da, Ligand)
Us10 (13 kDa, Protein from Homo sapiens)
El29 (17 kDa, Protein from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
El38 (8 kDa, Protein from Homo sapiens)
Plitidepsin (1 kDa, Ligand)
Ul11 (17 kDa, Protein from Homo sapiens)
El43 (10 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
El36 (12 kDa, Protein from Homo sapiens)
Us15 (17 kDa, Protein from Homo sapiens)
El15 (24 kDa, Protein from Homo sapiens)
El14 (23 kDa, Protein from Homo sapiens)
4-{(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4e,6z,10e)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione (457 Da, Ligand)
El8 (30 kDa, Protein from Homo sapiens)
El6 (32 kDa, Protein from Homo sapiens)
5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
El31 (14 kDa, Protein from Homo sapiens)
Ul15 (16 kDa, Protein from Homo sapiens)
Eef1a (50 kDa, Protein from Homo sapiens)
Us12 (15 kDa, Protein from Homo sapiens)
El24 (17 kDa, Protein from Homo sapiens)
Es25 (13 kDa, Protein from Homo sapiens)
Es31 (18 kDa, Protein from Homo sapiens)
Es17 (15 kDa, Protein from Homo sapiens)
Ul1 (24 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
18s rrna (603 kDa, RNA from Homo sapiens)
Es12 (14 kDa, Protein from Homo sapiens)
Es26 (13 kDa, Protein from Homo sapiens)
Human ribosome (Complex from Homo sapiens)
Es4 (29 kDa, Protein from Homo sapiens)
El22 (14 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
El20 (20 kDa, Protein from Homo sapiens)
El39 (6 kDa, Protein from Homo sapiens)
Ul13 (23 kDa, Protein from Homo sapiens)
El30 (12 kDa, Protein from Homo sapiens)
Us13 (17 kDa, Protein from Homo sapiens)
El32 (15 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
El21 (18 kDa, Protein from Homo sapiens)
Es19 (16 kDa, Protein from Homo sapiens)
Ul14 (14 kDa, Protein from Homo sapiens)

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EMD-14751

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Rabbit 80S ribosome as it decodes the Sec-UGA codon

Release date: Oct. 19, 2022
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7zjw
Q-score: 0.514

Hilal T, Killam BY, Grozdanovic M, Dobosz-Bartoszek M, Loerke J, Burger J, Mielke T, Copeland PR, Simonovic M, Spahn CMT

Science (2022) 376 pp. 1338-1343 [ Pubmed: 35709277 DOI: doi:10.1126/science.abg3875 ]

Sample:

60s ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el39 (6 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
80s-selenosome (3 MDa, Complex)
40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
Eefsec (67 kDa, Protein from Homo sapiens)
Eefsec and secis binding protein 2 (Complex from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el8 (30 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us11 (16 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
60s ribosomal protein el43 (10 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el18 (21 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
Water (18 Da, Ligand)
40s ribosomal protein s9 (22 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein ul2 (28 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el13 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el24 (17 kDa, Protein from Oryctolagus cuniculus)
Crpv ires (345 kDa, RNA from Cricket paralysis virus)
60s ribosomal protein ul23 (17 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
Gpx4 secis element (Complex from Rattus norvegicus)
40s ribosomal protein us14 (6 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el38 (8 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us15 (17 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein es21 (9 kDa, Protein from Oryctolagus cuniculus)
Human ser-trna-sec (28 kDa, RNA from Homo sapiens)
5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
Serine (105 Da, Ligand)
60s ribosomal protein el31 (14 kDa, Protein from Oryctolagus cuniculus)
Crpv ires (Complex from Cricket paralysis virus)
60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us9 (19 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el32 (15 kDa, Protein from Oryctolagus cuniculus)
Guanosine-5'-triphosphate (523 Da, Ligand)
40s ribosomal protein es19 (16 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein es4 (29 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el20 (20 kDa, Protein from Oryctolagus cuniculus)
Potassium ion (39 Da, Ligand)
60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el21 (18 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el30 (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el28 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
Zinc ion (65 Da, Ligand)
28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
Ribosomal protein es26 (13 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el22 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein ul29 (14 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us5 (31 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
Sodium ion (22 Da, Ligand)
60s ribosomal protein ul13 (23 kDa, Protein from Oryctolagus cuniculus)
18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
Ser-trna-sec (Complex from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein el33 (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein ul22 (21 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
Secis binding protein 2 (95 kDa, Protein from Homo sapiens)
60s ribosomal protein el42 (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l40 (14 kDa, Protein from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
Gpx4 secis element (275 kDa, RNA from Rattus norvegicus)
40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
80s ribosome (Complex from Oryctolagus cuniculus)
60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)

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