B. subtilis ApdA-stalled ribosomal complex
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8qcq
Q-score: 0.61
Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN
Nat Commun (2024) 15 pp. 2432-2432 [ DOI: doi:10.1038/s41467-024-46761-3 Pubmed: 38503735 ]
- Potassium ion (39 Da, Ligand)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 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 l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Mrna (1 kDa, RNA from Amycolatopsis japonica)
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Zinc ion (65 Da, Ligand)
- Pro-trna (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- Water (18 Da, Ligand)
- Proline (115 Da, Ligand)
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 23s rrna (948 kDa, RNA 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 l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l33 1 (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 l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Apda nascent chain (970 Da, Protein from Amycolatopsis japonica)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Small ribosomal subunit protein us3 (23 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Small ribosomal subunit protein us7 (17 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 l32 (6 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 s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 5s rrna (38 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Large ribosomal subunit protein bl31-a (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l36 (4 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 l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- B. subtilis apda-stalled ribosomal complex (Complex from Amycolatopsis japonica)
- 50s ribosomal protein l18 (12 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 [ DOI: doi:10.1038/s41586-024-07027-6 Pubmed: 38326618 ]
- 30s ribosomal protein s10 (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 s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 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 s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 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 s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 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 s9 (14 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 s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease 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 s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 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 [ DOI: doi:10.1038/s41586-024-07027-6 Pubmed: 38326618 ]
- 30s ribosomal protein s10 (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 s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA 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 s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 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 s19 (10 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 s9 (14 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 s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease 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 s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 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 [ DOI: doi:10.1038/s41586-024-07027-6 Pubmed: 38326618 ]
- 30s ribosomal protein s10 (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 s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 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 s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 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 s19 (10 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 s16 (10 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 s17 (10 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 s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease 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)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 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 [ DOI: doi:10.1038/s41586-024-07027-6 Pubmed: 38326618 ]
- 30s ribosomal protein s10 (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 s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rnase r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 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 s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 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 s19 (10 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 s16 (10 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 s17 (10 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 s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 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 [ DOI: doi:10.1038/s41586-024-07027-6 Pubmed: 38326618 ]
- 30s ribosomal protein s10 (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 s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rnase r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 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 s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 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 s19 (10 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 s16 (10 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 s17 (10 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 s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8akn
Q-score: 0.647
Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN
Nat Chem Biol (2023) 19 pp. 1072-1081 [ Pubmed: 36997646 DOI: doi:10.1038/s41589-023-01293-7 ]
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
- Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Phenylalanine-trna (24 kDa, RNA from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
- Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome (2 MDa, Complex from Escherichia coli BW25113)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli BW25113)
- Peptide chain release factor rf1 (40 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
- Isoleucine-trna (24 kDa, RNA from Escherichia coli BW25113)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
- Spermine (202 Da, Ligand)
- Mrna (2 kDa, RNA from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
- 2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8am9
Q-score: 0.594
Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN
Nat Chem Biol (2023) 19 pp. 1072-1081 [ Pubmed: 36997646 DOI: doi:10.1038/s41589-023-01293-7 ]
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
- Mrna (3 kDa, RNA from Escherichia coli BW25113)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
- Initiator trna (24 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
- Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
- Leucine trna (27 kDa, RNA from Escherichia coli BW25113)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
- Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome (2 MDa, Complex from Escherichia coli K-12)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
- Spermine (202 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
- 2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
Cryo-EM structure of the E.coli 70S ribosome in complex with the antibiotic Myxovalargin B.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b7y
Q-score: 0.556
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 [ Pubmed: 36603206 DOI: doi:10.1021/jacs.2c08816 ]
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
- Cryo-em structure of the e.coli 70s ribosome in complex with the antibiotic myxovalargin b. (2 MDa, Complex from Escherichia coli BW25113)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
- Water (18 Da, Ligand)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli K-12)
- Messenger rna (935 Da, RNA from Escherichia coli K-12)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli K-12)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
- Myxovalargin b (1 kDa, Protein from Myxococcus fulvus)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
- N-formylmethionine (177 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli K-12)
- P-trna fmet (24 kDa, RNA from Escherichia coli K-12)
- 16s ribosomal rna (496 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s18 (9 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 [ Pubmed: 34294725 DOI: doi:10.1038/s41467-021-24674-9 ]
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- Mrna (1 kDa, RNA from Escherichia coli)
- Ermdl (877 Da, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- Erythromycin a (733 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- A-trna (arg) (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 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 s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (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)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- P-trna (leu) (28 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s13 (12 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 l16 (15 kDa, Protein from Escherichia coli)