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Escherichia coli 50S subunit in complex with the antimicrobial peptide Api137
Lauer SM, Reepmeyer M, Berendes O, Klepacki D, Gasse J, Gabrielli S, Grubmuller H, Bock LV, Krizsan A, Nikolay R, Spahn CMT, Hoffmann R
Nat Commun (2024) 15 pp. 3945-3945 [ Pubmed: 38730238 DOI: doi:10.1038/s41467-024-48027-4 ]
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl33 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Api137 in complex with the large ribosomal subunit (Complex)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit (Complex from Escherichia coli)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Escherichia coli)
- Apidaecins type 137 (2 kDa, Protein from Apis mellifera)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- Api137 (Complex from Apis mellifera)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl27 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
Escherichia coli 50S subunit in complex with the antimicrobial peptide Api88 - conformation I
Lauer SM, Reepmeyer M, Berendes O, Klepacki D, Gasse J, Gabrielli S, Grubmuller H, Bock LV, Krizsan A, Nikolay R, Spahn CMT, Hoffmann R
Nat Commun (2024) 15 pp. 3945-3945 [ Pubmed: 38730238 DOI: doi:10.1038/s41467-024-48027-4 ]
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl33 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Apidaecins type 88 (2 kDa, Protein from Apis mellifera)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit (Complex from Escherichia coli)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Escherichia coli)
- Api88 in complex with the large ribosomal subunit - conformation i (Complex)
- Large ribosomal subunit protein ul15 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Api88 (Complex from Apis mellifera)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl27 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
Escherichia coli 50S subunit in complex with the antimicrobial peptide Api88 - conformation II
Lauer SM, Reepmeyer M, Berendes O, Klepacki D, Gasse J, Gabrielli S, Grubmuller H, Bock LV, Krizsan A, Nikolay R, Spahn CMT, Hoffmann R
Nat Commun (2024) 15 pp. 3945-3945 [ Pubmed: 38730238 DOI: doi:10.1038/s41467-024-48027-4 ]
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl33 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Apidaecins type 88 (2 kDa, Protein from Apis mellifera)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit (Complex from Escherichia coli)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Api88 (Complex from Apis mellifera)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- Api88 in complex with the large ribosomal subunit - conformation ii (Complex)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl27 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
Escherichia coli 50S subunit in complex with the antimicrobial peptide Api88 - conformation III
Lauer SM, Reepmeyer M, Berendes O, Klepacki D, Gasse J, Gabrielli S, Grubmuller H, Bock LV, Krizsan A, Nikolay R, Spahn CMT, Hoffmann R
Nat Commun (2024) 15 pp. 3945-3945 [ Pubmed: 38730238 DOI: doi:10.1038/s41467-024-48027-4 ]
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl33 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Apidaecins type 88 (2 kDa, Protein from Apis mellifera)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Api88 in complex with the large ribosomal subunit - conformation iii (Complex)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit (Complex from Escherichia coli)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Api88 (Complex from Apis mellifera)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl27 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
E. coli ApdP-stalled ribosomal complex
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8qbt
Q-score: 0.611
Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN
Nat Commun (2024) 15 pp. 2432-2432 [ Pubmed: 38503735 DOI: doi:10.1038/s41467-024-46761-3 ]
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli BW25113)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli BW25113)
- E. coli apdp-stalled ribosomal complex (Complex from Sinorhizobium medicae)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli BW25113)
- Proline (115 Da, Ligand)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli BW25113)
- Apdp nascent chain (688 Da, Protein from Sinorhizobium medicae)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli BW25113)
- Pro-trna (24 kDa, RNA from Escherichia coli BW25113)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Mrna (3 kDa, RNA from Sinorhizobium medicae)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli BW25113)
- 5s rrna (38 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli BW25113)
- Ala-trna (24 kDa, RNA from Escherichia coli BW25113)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
Structure of SecM-stalled Escherichia coli 70S ribosome
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8qoa
Q-score: 0.652
Gersteuer F, Morici M, Gabrielli S, Fujiwara K, Safdari HA, Paternoga H, Bock LV, Chiba S, Wilson DN
Nat Commun (2024) 15 pp. 2431-2431 [ DOI: doi:10.1038/s41467-024-46762-2 Pubmed: 38503753 ]
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli BW25113)
- Secm-stalled ribosome complex (Complex from Escherichia coli BW25113)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli BW25113)
- Proline (115 Da, Ligand)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli BW25113)
- Secretion monitor (3 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- P-site trna-gly (24 kDa, RNA from Escherichia coli BW25113)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli BW25113)
- E-site trna (589 Da, RNA from Escherichia coli BW25113)
- A-site trna-pro (24 kDa, RNA from Escherichia coli BW25113)
- 5s rrna (38 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli BW25113)
- Zinc ion (65 Da, Ligand)
- Mrna (2 kDa, RNA from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli BW25113)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli BW25113)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HPF (structure I-A)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8uu4
Q-score: 0.508
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ DOI: doi:10.1093/nar/gkae128 Pubmed: 38407413 ]
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Ribosome hibernation promoting factor (21 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
- Listeria innocua 70s ribosome bound to hpf (2 MDa, Complex from Listeria innocua)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8uu5
Q-score: 0.552
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ DOI: doi:10.1093/nar/gkae128 Pubmed: 38407413 ]
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Listeria innocua 70s ribosome in complex with pe/e-trna (2 MDa, Complex from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- F-stop mrna (6 kDa, RNA from Escherichia phage T4)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Pe/e hybrid state phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8uu6
Q-score: 0.489
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ DOI: doi:10.1093/nar/gkae128 Pubmed: 38407413 ]
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Listeria innocua 70s ribosome in complex with p/e-trna (2 MDa, Complex from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Potassium ion (39 Da, Ligand)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- P/e hybrid state phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- F-stop mrna (6 kDa, RNA from Escherichia phage T4)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8uu7
Q-score: 0.512
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ DOI: doi:10.1093/nar/gkae128 Pubmed: 38407413 ]
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Ribosome hibernation promoting factor (21 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Listeria innocua 70s ribosome in complex with hpf, hflxr and e-site trna (2 MDa, Complex from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Gtpase hflx (47 kDa, Protein from Listeria monocytogenes EGD-e)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- E-site phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)