Resolution: 1.96 Å
EM Method: Single-particle
Fitted PDBs: 8s1p
Q-score: 0.688
Takada H, Paternoga H, Fujiwara K, Nakamoto JA, Park EN, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk AR, Atkinson GC, Chiba S, Wilson DN, Hauryliuk V
Nucleic Acids Res (2024) 52 pp. 8483-8499 [ DOI: doi:10.1093/nar/gkae399 Pubmed: 38811035 ]
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Nascent chain (358 Da, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 5s rrna (36 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Chloramphenicol (323 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Water (18 Da, Ligand)
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- P-trna (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal subunit with stalled p-trna-nascent chain, bound by ylmh (Complex from Bacillus subtilis subsp. subtilis str. 168)
- Putative rna-binding protein ylmh (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
YlmH bound to stalled 50S subunits with RqcH and PtRNA
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8s1u
Q-score: 0.448
Takada H, Paternoga H, Fujiwara K, Nakamoto JA, Park EN, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk AR, Atkinson GC, Chiba S, Wilson DN, Hauryliuk V
Nucleic Acids Res (2024) 52 pp. 8483-8499 [ DOI: doi:10.1093/nar/gkae399 Pubmed: 38811035 ]
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 5s rrna (36 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- P-trna (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal subunit with stalled p-trna-nascent chain, bound by ylmh (Complex from Bacillus subtilis subsp. subtilis str. 168)
- Putative rna-binding protein ylmh (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rqc2 homolog rqch (65 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (main state)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8cdu
Q-score: 0.468
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (state II)
Resolution: 4.73 Å
EM Method: Single-particle
Fitted PDBs: 8cdv
Q-score: 0.272
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (3 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8cec
Q-score: 0.388
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Resolution: 4.15 Å
EM Method: Single-particle
Fitted PDBs: 8ced
Q-score: 0.265
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rnase r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8cee
Q-score: 0.298
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rnase r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A.
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 7qq3
Q-score: 0.588
Koller TO, Scheid U, Kosel T, Herrmann J, Krug D, Boshoff HIM, Beckert B, Evans JC, Schlemmer J, Sloan B, Weiner DM, Via LE, Moosa A, Ioerger TR, Graf M, Zinshteyn B, Abdelshahid M, Nguyen F, Arenz S, Gille F, Siebke M, Seedorf T, Plettenburg O, Green R, Warnke AL, Ullrich J, Warrass R, Barry 3rd CE, Warner DF, Mizrahi V, Kirschning A, Wilson DN, Muller R
J Am Chem Soc (2023) 145 pp. 851-863 [ DOI: doi:10.1021/jacs.2c08816 Pubmed: 36603206 ]
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
- Cryo-em structure of the e.coli 50s ribosomal subunit in complex with the antibiotic myxovalargin a. (1 MDa, Complex from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
- Myxovalargin a (1 kDa, Protein from Myxococcus fulvus)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
- Water (18 Da, Ligand)
- 50s ribosomal protein l15 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with A and P-tRNA
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7nsp
Q-score: 0.448
Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmuller H, Mankin AS, Innis CA, Vazquez-Laslop N, Wilson DN
Nat Commun (2021) 12 pp. 4466-4466 [ DOI: doi:10.1038/s41467-021-24674-9 Pubmed: 34294725 ]
- A-trna (arg) (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- Ermdl (877 Da, Protein from Escherichia coli)
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- P-trna (leu) (28 kDa, RNA from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- Structure of ermdl-erythromycin-stalled 70s e. coli ribosomal complex with a and p-trna (Complex from Escherichia coli)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- Mrna (1 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- Erythromycin a (733 Da, Ligand)
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with P-tRNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nso
Q-score: 0.551
Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmuller H, Mankin AS, Innis CA, Vazquez-Laslop N, Wilson DN
Nat Commun (2021) 12 pp. 4466-4466 [ DOI: doi:10.1038/s41467-021-24674-9 Pubmed: 34294725 ]
- 23s rrna (2903-mer) (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 16s rrna (1540-mer) (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- Ermdl (877 Da, Protein from Escherichia coli)
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
- Ptrna-leu (28 kDa, RNA from Escherichia coli)
- Structure of ermdl-erythromycin-stalled 70s e. coli ribosomal complex with p-trna (Complex from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- Mrna (872 Da, RNA from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- Erythromycin a (733 Da, Ligand)
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)