Mycobacterium smegmatis 50S ribosomal subunit-HflX complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8kab
Q-score: 0.419
Srinivasan K, Banerjee A, Sengupta J
Structure (2024) 32 pp. 1443- [ DOI: doi:10.1016/j.str.2024.06.016 Pubmed: 39029461 ]
- 50s ribosomal protein bl37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l10 (18 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l3 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit-hflx complex (Complex from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l33 1 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l17 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l22 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Gtpase hflx (52 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l23 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s rrna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- 50s ribosomal protein l28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l11 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l30 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s rrna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis hflx (Cellular component from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit (Cellular component from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l21 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l31 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterium smegmatis 50S ribosomal subunit with Erythromycin
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8xz3
Q-score: 0.473
Srinivasan K, Banerjee A, Sengupta J
Structure (2024) 32 pp. 1443- [ DOI: doi:10.1016/j.str.2024.06.016 Pubmed: 39029461 ]
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit-erythromycin complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl21 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl31 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul10 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Erythromycin a (733 Da, Ligand)
- Large ribosomal subunit protein bl33a (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl27 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s rrna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s rrna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl25 (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul11 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein bl37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit (Cellular component from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mouse RPL39L integrated into the yeast 60S ribosomal subunit
Resolution: 2.15 Å
EM Method: Single-particle
Fitted PDBs: 8pfr
Q-score: 0.675
Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M
Nucleic Acids Res (2024) 52 pp. 9028-9048 [ Pubmed: 39041433 DOI: doi:10.1093/nar/gkae630 ]
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Mouse rpl39l in yeast 60s ribosomal subunit (1 MDa, Complex from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- Chloride ion (35 Da, Ligand)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l39-like (6 kDa, Protein from Mus musculus)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l38 (8 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)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
Yeast 60S ribosomal subunit, RPL39 deletion
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8p8m
Q-score: 0.571
Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M
Nucleic Acids Res (2024) 52 pp. 9028-9048 [ Pubmed: 39041433 DOI: doi:10.1093/nar/gkae630 ]
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- Yeast 60s ribosomal subunit without ribosomal protein rpl39 (1 MDa, Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 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)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
Mouse RPL39 integrated into the yeast 60S ribosomal subunit
Resolution: 2.15 Å
EM Method: Single-particle
Fitted PDBs: 8p8n
Q-score: 0.665
Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M
Nucleic Acids Res (2024) 52 pp. 9028-9048 [ DOI: doi:10.1093/nar/gkae630 Pubmed: 39041433 ]
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Mouse rpl39 integrated into yeast 60s ribosomal subunit (1 MDa, Complex from Saccharomyces cerevisiae)
- Chloride ion (35 Da, Ligand)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Mus musculus)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 2.23 Å
EM Method: Single-particle
Fitted PDBs: 8p8u
Q-score: 0.653
Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M
Nucleic Acids Res (2024) 52 pp. 9028-9048 [ DOI: doi:10.1093/nar/gkae630 Pubmed: 39041433 ]
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Chloride ion (35 Da, Ligand)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- Yeast 60s ribosomal subunit (1 MDa, Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8sq9
Q-score: 0.528
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ Pubmed: 37890482 DOI: doi:10.1016/j.molcel.2023.10.001 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 replication-transcription complex bound to nsp9 and umpcpp, as a pre-catalytic nmpylation intermediate (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine (482 Da, Ligand)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8sqj
Q-score: 0.511
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ Pubmed: 37890482 DOI: doi:10.1016/j.molcel.2023.10.001 ]
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- 5'-o-[(r)-hydroxy(thiophosphonooxy)phosphoryl]guanosine (459 Da, Ligand)
- Template rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 replication-transcription complex bound to rna-nsp9, as a noncatalytic rna-nsp9 binding mode (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8sqk
Q-score: 0.533
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ Pubmed: 37890482 DOI: doi:10.1016/j.molcel.2023.10.001 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase nsp12 (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 5'-o-[(r)-hydroxy(thiophosphonooxy)phosphoryl]guanosine (459 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Primer rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Sars-cov-2 replication-transcription complex bound to rna-nsp9 and gdp-betas, as a pre-catalytic dernaylation/mrna capping intermediate (Complex from Severe acute respiratory syndrome coronavirus 2)
Prefusion-stabilized SARS-CoV-2 spike protein
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8fez
Q-score: 0.312
Gonzalez KJ, Huang J, Criado MF, Banerjee A, Tompkins SM, Mousa JJ, Strauch EM
Nat Commun (2024) 15 pp. 1335-1335 [ DOI: doi:10.1038/s41467-024-45480-z Pubmed: 38351001 ]