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 l30 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l17 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l21 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l22 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s rrna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 5s rrna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l31 (8 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 l20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit-hflx complex (Complex from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Gtpase hflx (52 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l11 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein bl37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l3 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l23 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis hflx (Cellular component from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l10 (18 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit (Cellular component from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l2 (30 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 bl21 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl25 (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s rrna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein bl37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s rrna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul11 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl31 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul10 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit-erythromycin complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl33a (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 50s ribosomal subunit (Cellular component from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Erythromycin a (733 Da, Ligand)
- Large ribosomal subunit protein bl27 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul24 (11 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 [ DOI: doi:10.1093/nar/gkae630 Pubmed: 39041433 ]
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l39-like (6 kDa, Protein from Mus musculus)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Mouse rpl39l in yeast 60s ribosomal subunit (1 MDa, Complex from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- Chloride ion (35 Da, Ligand)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
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 [ DOI: doi:10.1093/nar/gkae630 Pubmed: 39041433 ]
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Yeast 60s ribosomal subunit without ribosomal protein rpl39 (1 MDa, Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s acidic ribosomal protein p0 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 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)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
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 l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- Mouse rpl39 integrated into yeast 60s ribosomal subunit (1 MDa, Complex from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Mus musculus)
- Chloride ion (35 Da, Ligand)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 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 l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l24-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae)
- Yeast 60s ribosomal subunit (1 MDa, Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
- Chloride ion (35 Da, Ligand)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l10 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 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 [ DOI: doi:10.1016/j.molcel.2023.10.001 Pubmed: 37890482 ]
- Template rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Water (18 Da, Ligand)
- Non-structural protein 9 (12 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)
- Magnesium ion (24 Da, Ligand)
- 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)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine (482 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 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 [ DOI: doi:10.1016/j.molcel.2023.10.001 Pubmed: 37890482 ]
- Template rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- 5'-o-[(r)-hydroxy(thiophosphonooxy)phosphoryl]guanosine (459 Da, Ligand)
- Water (18 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- 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)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 5' utr (6 kDa, RNA 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)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1016/j.molcel.2023.10.001 Pubmed: 37890482 ]
- 5'-o-[(r)-hydroxy(thiophosphonooxy)phosphoryl]guanosine (459 Da, Ligand)
- 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)
- Water (18 Da, Ligand)
- Rna-directed rna polymerase nsp12 (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Template rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Zinc ion (65 Da, Ligand)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8di5
Q-score: 0.51
Chen C, Saville JW, Marti MM, Schafer A, Cheng MH, Mannar D, Zhu X, Berezuk AM, Banerjee A, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Enick N, McCormick KD, Liu X, Adams C, Hines MG, Sun Z, Chen W, Jacobs JL, Barratt-Boyes SM, Mellors JW, Baric RS, Bahar I, Dimitrov DS, Subramaniam S, Martinez DR, Li W
iScience (2022) 25 pp. 104798-104798 [ DOI: doi:10.1016/j.isci.2022.104798 Pubmed: 35875685 ]
- Sars-cov-2 beta (b.1.351) spike protein in complex with vh domain f6 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Vh f6 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Vh f6 (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 beta (b.1.351) spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)