Retapamulin and Capreomycin bound to the 50S subunit
Resolution: 1.83 Å
EM Method: Single-particle
Fitted PDBs: 8ceu
Q-score: 0.756
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ DOI: doi:10.1038/s41594-023-01047-y Pubmed: 37550453 ]
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli BW25113)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli BW25113)
- 5s rrna (38 kDa, RNA from Escherichia coli BW25113)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli BW25113)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
- Capreomycin ia (686 Da, Protein from Streptomyces californicus)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli BW25113)
- Retapamulin (517 Da, Ligand)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli BW25113)
Clindamycin bound to the 50S subunit
Resolution: 1.98 Å
EM Method: Single-particle
Fitted PDBs: 8cgd
Q-score: 0.752
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ DOI: doi:10.1038/s41594-023-01047-y Pubmed: 37550453 ]
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli BW25113)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli BW25113)
- 5s rrna (38 kDa, RNA from Escherichia coli BW25113)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli BW25113)
- Clindamycin (424 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli BW25113)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
- Acetate ion (59 Da, Ligand)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli BW25113)
- Apramycin (539 Da, Ligand)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli BW25113)
mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)
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 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]
- Es7 (22 kDa, Protein from Homo sapiens)
- Es25 (13 kDa, Protein from Homo sapiens)
- Rack1 (35 kDa, Protein from Homo sapiens)
- Es4 (29 kDa, Protein from Homo sapiens)
- El8 (30 kDa, Protein from Homo sapiens)
- El40 (14 kDa, Protein from Homo sapiens)
- El32 (15 kDa, Protein from Homo sapiens)
- Us3 (26 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- El30 (12 kDa, Protein from Homo sapiens)
- Es26 (13 kDa, Protein from Homo sapiens)
- Es24 (15 kDa, Protein from Homo sapiens)
- Us19 (17 kDa, Protein from Homo sapiens)
- Methionine (149 Da, Ligand)
- El34 (13 kDa, Protein from Homo sapiens)
- El24 (17 kDa, Protein from Homo sapiens)
- Us10 (13 kDa, Protein from Homo sapiens)
- Ul6 (21 kDa, Protein from Homo sapiens)
- El33 (12 kDa, Protein from Homo sapiens)
- El18 (21 kDa, Protein from Homo sapiens)
- Es19 (16 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- El14 (23 kDa, Protein from Homo sapiens)
- Ul29 (14 kDa, Protein from Homo sapiens)
- Spermidine (145 Da, Ligand)
- Es6 (28 kDa, Protein from Homo sapiens)
- Ul13 (23 kDa, Protein from Homo sapiens)
- El20 (20 kDa, Protein from Homo sapiens)
- Us7 (22 kDa, Protein from Homo sapiens)
- El15 (24 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Us9 (16 kDa, Protein from Homo sapiens)
- Us5 (31 kDa, Protein from Homo sapiens)
- Ul5 (20 kDa, Protein from Homo sapiens)
- Es8 (24 kDa, Protein from Homo sapiens)
- Us12 (15 kDa, Protein from Homo sapiens)
- Eef1a (50 kDa, Protein from Homo sapiens)
- Us8 (14 kDa, Protein from Homo sapiens)
- Ul15 (16 kDa, Protein from Homo sapiens)
- Us11 (16 kDa, Protein from Homo sapiens)
- Es27 (9 kDa, Protein from Homo sapiens)
- 1,4-diaminobutane (88 Da, Ligand)
- Ul11 (17 kDa, Protein from Homo sapiens)
- El38 (8 kDa, Protein from Homo sapiens)
- El41 (3 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)
- P-site trna (24 kDa, RNA from Homo sapiens)
- Es28 (7 kDa, Protein from Homo sapiens)
- A-site trna (24 kDa, RNA from Homo sapiens)
- Es21 (9 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- El22 (14 kDa, Protein from Homo sapiens)
- Ul23 (17 kDa, Protein from Homo sapiens)
- El19 (23 kDa, Protein from Homo sapiens)
- Phenylalanine (165 Da, Ligand)
- El6 (32 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- El28 (15 kDa, Protein from Homo sapiens)
- El27 (15 kDa, Protein from Homo sapiens)
- Ul3 (46 kDa, Protein from Homo sapiens)
- Human ribosome (Complex from Homo sapiens)
- El31 (14 kDa, Protein from Homo sapiens)
- El42 (12 kDa, Protein from Homo sapiens)
- El39 (6 kDa, Protein from Homo sapiens)
- 5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
- Ul14 (14 kDa, Protein from Homo sapiens)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- El37 (11 kDa, Protein from Homo sapiens)
- Ul22 (21 kDa, Protein from Homo sapiens)
- Plitidepsin (1 kDa, Ligand)
- Ul1 (24 kDa, Protein from Homo sapiens)
- Mrna (19 kDa, RNA from Homo sapiens)
- El43 (10 kDa, Protein from Homo sapiens)
- El13 (31 kDa, Protein from Homo sapiens)
- Ul18 (34 kDa, Protein from Homo sapiens)
- Us2 (32 kDa, Protein from Homo sapiens)
- El36 (12 kDa, Protein from Homo sapiens)
- Ul16 (24 kDa, Protein from Homo sapiens)
- Us14 (6 kDa, Protein from Homo sapiens)
- Es30 (14 kDa, Protein from Homo sapiens)
- Es31 (18 kDa, Protein from Homo sapiens)
- Es17 (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Es10 (18 kDa, Protein from Homo sapiens)
- Us15 (17 kDa, Protein from Homo sapiens)
- Ul4 (47 kDa, Protein from Homo sapiens)
- Es1 (30 kDa, Protein from Homo sapiens)
- Ul10 (34 kDa, Protein from Homo sapiens)
- Ul30 (29 kDa, Protein from Homo sapiens)
- El21 (18 kDa, Protein from Homo sapiens)
- Ul2 (28 kDa, Protein from Homo sapiens)
- Us4 (22 kDa, Protein from Homo sapiens)
- Anisomycin (265 Da, Ligand)
- Us17 (18 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Us13 (17 kDa, Protein from Homo sapiens)
- Ul24 (17 kDa, Protein from Homo sapiens)
- El29 (17 kDa, Protein from Homo sapiens)
- Es12 (14 kDa, Protein from Homo sapiens)