Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8k2d
Q-score: 0.423
Li X, Wang M, Denk T, Buschauer R, Li Y, Beckmann R, Cheng J
Nat Commun (2024) 15 pp. 5481-5481 [ DOI: doi:10.1038/s41467-024-49797-7 Pubmed: 38942792 ]
- 23s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul18 (33 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el24a (17 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us7 (25 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul3 (43 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el6a (20 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul30a (27 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul22a (20 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el37a (9 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us13a (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el32 (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul23 (15 kDa, Protein from Saccharomyces cerevisiae)
- Suppressor protein stm1 (30 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el43a (10 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el41a (3 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul4a (39 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es21a (9 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el22a (13 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul29a (13 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el36a (11 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us9a (15 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es26b (13 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el34a (13 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us14a (6 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul1a (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Elongation factor 2 (93 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Large ribosomal subunit protein el30 (11 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el8a (28 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul10 (33 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul15 (16 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us10 (13 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-ribosomal protein el40a fusion protein (14 kDa, Protein from Saccharomyces cerevisiae)
- Eukaryotic translation initiation factor 5a-1 (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el13a (22 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul14a (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul5a (19 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es17a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el18a (20 kDa, Protein from Saccharomyces cerevisiae)
- Yeast 80s ribosome (Complex from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us17a (17 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el42a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul24a (14 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 18s rrna (579 kDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es19a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es25a (12 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us2a (28 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul16 (25 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul2a (27 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es28a (7 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-ribosomal protein es31 fusion protein (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el31a (12 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el29 (6 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el20a (20 kDa, Protein from Saccharomyces cerevisiae)
- Tigecycline (587 Da, Ligand)
- Large ribosomal subunit protein el15a (24 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us19 (16 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el19a (21 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es12 (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el27a (15 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es10a (12 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el14a (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul6a (21 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el33a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el21a (18 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul11a (17 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein rack1 (34 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul13a (22 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el38 (8 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8k82
Q-score: 0.453
Li X, Wang M, Denk T, Buschauer R, Li Y, Beckmann R, Cheng J
Nat Commun (2024) 15 pp. 5481-5481 [ DOI: doi:10.1038/s41467-024-49797-7 Pubmed: 38942792 ]
- 23s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul18 (33 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el24a (17 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us7 (25 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul3 (43 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el6a (20 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul30a (27 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul22a (20 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el37a (9 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us13a (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el32 (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul23 (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el43a (10 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el41a (3 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul4a (39 kDa, Protein from Saccharomyces cerevisiae)
- Trna (24 kDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es21a (9 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el22a (13 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul29a (13 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el36a (11 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us9a (15 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es26b (13 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el34a (13 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us14a (6 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul1a (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein el30 (11 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el8a (28 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul10 (33 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul15 (16 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us10 (13 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-ribosomal protein el40a fusion protein (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el13a (22 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul14a (14 kDa, Protein from Saccharomyces cerevisiae)
- General negative regulator of transcription subunit 5 (65 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul5a (19 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es17a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el18a (20 kDa, Protein from Saccharomyces cerevisiae)
- Yeast 80s ribosome (Complex from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us17a (17 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el42a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul24a (14 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 18s rrna (579 kDa, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es19a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es25a (12 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us2a (28 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul16 (25 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul2a (27 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es28a (7 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-ribosomal protein es31 fusion protein (17 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el31a (12 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el29 (6 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el20a (20 kDa, Protein from Saccharomyces cerevisiae)
- Tigecycline (587 Da, Ligand)
- Large ribosomal subunit protein el15a (24 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us19 (16 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el19a (21 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es12 (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el27a (15 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es10a (12 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el14a (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul6a (21 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el33a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el21a (18 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul11a (17 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Mrna (935 Da, RNA from Saccharomyces cerevisiae)
- Small ribosomal subunit protein rack1 (34 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul13a (22 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el38 (8 kDa, Protein from Saccharomyces cerevisiae)
Front Mol Biosci (2024) 11 pp. 1395220-1395220 [ DOI: doi:10.3389/fmolb.2024.1395220 Pubmed: 38698775 ]
Front Mol Biosci (2024) 11 pp. 1395220-1395220 [ DOI: doi:10.3389/fmolb.2024.1395220 Pubmed: 38698775 ]
Front Mol Biosci (2024) 11 pp. 1395220-1395220 [ DOI: doi:10.3389/fmolb.2024.1395220 Pubmed: 38698775 ]
NuA4 HAT module bound to the nucleosome
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7vvu
Q-score: 0.314
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae)
- H4 (11 kDa, Protein from Xenopus laevis)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Complex of nua4 hat module and nucleosome (Complex from Saccharomyces cerevisiae)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7vvy
Q-score: 0.384
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae S288C)
- Tra1 module of nua4 (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 8.8 Å
EM Method: Single-particle
Fitted PDBs: 7vvz
Q-score: 0.108
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nua4 bound to the nucleosome (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- Epl1 arginine anchor (1 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae S288C)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)