Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8uu5
Q-score: 0.552
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ Pubmed: 38407413 DOI: doi:10.1093/nar/gkae128 ]
- Listeria innocua 70s ribosome in complex with pe/e-trna (2 MDa, Complex from Listeria innocua)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 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)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- F-stop mrna (6 kDa, RNA from Escherichia phage T4)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Pe/e hybrid state phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us14 (7 kDa, Protein 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 ]
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Listeria innocua 70s ribosome in complex with p/e-trna (2 MDa, Complex from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Potassium ion (39 Da, Ligand)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
- P/e hybrid state phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- F-stop mrna (6 kDa, RNA from Escherichia phage T4)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein 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 [ Pubmed: 38407413 DOI: doi:10.1093/nar/gkae128 ]
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Ribosome hibernation promoting factor (21 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Gtpase hflx (47 kDa, Protein from Listeria monocytogenes EGD-e)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Listeria innocua 70s ribosome in complex with hpf, hflxr and e-site trna (2 MDa, Complex from Listeria innocua)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- E-site phenylalanine trna (24 kDa, RNA from Escherichia coli)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 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)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8uu8
Q-score: 0.496
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ Pubmed: 38407413 DOI: doi:10.1093/nar/gkae128 ]
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul10 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Gtpase hflx (47 kDa, Protein from Listeria monocytogenes EGD-e)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul11 (14 kDa, Protein from Listeria innocua)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
- Listeria innocua 70s ribosome in complex with hflxr and pe/e-trna (2 MDa, Complex from Listeria innocua)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- F-stop mrna (6 kDa, RNA from Escherichia phage T4)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Pe/e hybrid state phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8uu9
Q-score: 0.495
Nucleic Acids Res (2024) 52 pp. 4053-4066 [ Pubmed: 38407413 DOI: doi:10.1093/nar/gkae128 ]
- Small ribosomal subunit protein us5 (17 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Listeria innocua)
- 5s ribosomal rna (37 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein bl27 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl31b (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul16 (16 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Listeria innocua)
- 23s ribosomal rna (951 kDa, RNA from Listeria innocua)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs6 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Listeria innocua)
- Magnesium ion (24 Da, Ligand)
- Gtpase hflx (47 kDa, Protein from Listeria monocytogenes EGD-e)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Listeria innocua)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Listeria innocua)
- Pe/e hybrid state phenylalanine trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Listeria innocua)
- 16s ribosomal rna (501 kDa, RNA from Listeria innocua)
- Listeria innocua 70s ribosome in complex with hflxr and pe/e-trna (2 MDa, Complex from Listeria innocua)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Listeria innocua)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us3 (24 kDa, Protein from Listeria innocua)
- F-stop mrna (6 kDa, RNA from Escherichia phage T4)
- Large ribosomal subunit protein bl17 (15 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl28 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us2 (28 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Listeria innocua)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein bs16 (10 kDa, Protein from Listeria innocua)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Listeria innocua)
- Small ribosomal subunit protein us14 (7 kDa, Protein from Listeria innocua)
Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8u3b
Q-score: 0.454
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B
Nucleic Acids Res (2024) 52 pp. 1471-1482 [ DOI: doi:10.1093/nar/gkad1231 Pubmed: 38197271 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Nitrate/nitrite response regulator protein narl (8 kDa, Protein from Escherichia coli)
- Dna (69-mer) (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna (69-mer) (21 kDa, DNA from Escherichia coli)
- E. coli narl transcription activation complex on the year promoter (625 kDa, Complex from Escherichia coli)
- Rna (5'-d(*(gtp))-r(p*ap*a)-3') (1 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8pvv
Q-score: 0.56
Manakova E, Golovinas E, Poceviciute R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaite E, Jurgelaitis E, Grybauskas A, Venclovas C, Zaremba M
Nucleic Acids Res (2024) 52 pp. 2530-2545 [ DOI: doi:10.1093/nar/gkad1241 Pubmed: 38197228 ]
- Archaeoglobus fulgidus afago-n protein (Complex from Archaeoglobus fulgidus DSM 8774)
- Afago and afago-n complex with 30 nt rna guide and 51 nt dna target (90 kDa, Complex)
- Rna (30-mer) (Complex from Escherichia coli)
- Piwi protein (49 kDa, Protein from Archaeoglobus fulgidus)
- Piwi protein (Complex from Archaeoglobus fulgidus)
- Archaeoglobus fulgidus afago-n protein (31 kDa, Protein from Archaeoglobus fulgidus DSM 8774)
- Water (18 Da, Ligand)
- Rna (30-mer) (9 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (51-mer) (15 kDa, DNA from Escherichia coli)
- Dna (51-mer) (Complex from Escherichia coli)
Structural insights into the binding of bS1 to the ribosome
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 8a3l
Q-score: 0.46
D'Urso G, Chat S, Gillet R, Giudice E
Nucleic Acids Res (2023) 51 pp. 3410-3419 [ Pubmed: 36840711 DOI: doi:10.1093/nar/gkad126 ]
- Mrna (12 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l31 (7 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)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
- P-site fmet-trna(fmet) (24 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
- 16s ribosomal rna (498 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s1 (61 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
- E-site trna (24 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli K-12)
- Elongation competent ribosome in complex with bs1 (2 GDa, Complex from Escherichia coli)
Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8crx
Q-score: 0.519
Lomakin IB, Devarkar SC, Patel S, Grada A, Bunick CG
Nucleic Acids Res (2023) 51 pp. 2915-2930 [ Pubmed: 36864821 DOI: doi:10.1093/nar/gkad103 ]
- 30s ribosomal protein s12 (13 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s6 (11 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s4 (23 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s15 (10 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l13 (16 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l22 (16 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l5 (23 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l30 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l23 (11 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s3 (29 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l29 (8 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s8 (14 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s11 (14 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s7 (17 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l4 (32 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l14 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l28 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l16 (15 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l21 (11 kDa, Protein from Cutibacterium acnes)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l31 (7 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l3 (23 kDa, Protein from Cutibacterium acnes)
- 70s ribosome with mrna, p-site trna and sarecycline bound (Complex from Cutibacterium acnes)
- 30s ribosomal protein s13 (14 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l15 (15 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein bl37 (2 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l32 (6 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s17 (10 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l24 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l2 (30 kDa, Protein from Cutibacterium acnes)
- Water (18 Da, Ligand)
- 50s ribosomal protein l34 (5 kDa, Protein from Cutibacterium acnes)
- 32mf mrna (7 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l17 (20 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l18 (13 kDa, Protein from Cutibacterium acnes)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l33 (6 kDa, Protein from Cutibacterium acnes)
- 5s ribosomal rna (38 kDa, RNA from Cutibacterium acnes)
- 50s ribosomal protein l35 (7 kDa, Protein from Cutibacterium acnes)
- Sarecycline (487 Da, Ligand)
- 30s ribosomal protein s19 (10 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s5 (22 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l19 (13 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s10 (11 kDa, Protein from Cutibacterium acnes)
- 23s ribosomal rna (1 MDa, RNA from Cutibacterium acnes)
- 30s ribosomal protein s2 (31 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l20 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l25 (22 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l6 (19 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s18 (8 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s20 (9 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s16 (15 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l27 (9 kDa, Protein from Cutibacterium acnes)
- P-site initiator trna (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Cutibacterium acnes)
- Rna (1537-mer) (498 kDa, RNA from Cutibacterium acnes)
- 30s ribosomal protein s14 type z (6 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein s9 (18 kDa, Protein from Cutibacterium acnes)
- 30s ribosomal protein bs22 (4 kDa, Protein from Cutibacterium acnes)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8cvm
Q-score: 0.565
Lomakin IB, Devarkar SC, Patel S, Grada A, Bunick CG
Nucleic Acids Res (2023) 51 pp. 2915-2930 [ DOI: doi:10.1093/nar/gkad103 Pubmed: 36864821 ]
- 50s subunit from 70s ribosome with mrna, p-site trna and sarecycline bound (Complex from Cutibacterium acnes)
- 50s ribosomal protein l20 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l35 (7 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l24 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l19 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l13 (16 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l23 (11 kDa, Protein from Cutibacterium acnes)
- Sarecycline (487 Da, Ligand)
- 50s ribosomal protein l34 (5 kDa, Protein from Cutibacterium acnes)
- Initiator fmet rna (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein bl37 (2 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l16 (15 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l17 (20 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l36 (4 kDa, Protein from Cutibacterium acnes)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l29 (8 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l31 (7 kDa, Protein from Cutibacterium acnes)
- 5s ribosomal rna (38 kDa, RNA from Cutibacterium acnes)
- 50s ribosomal protein l21 (11 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l22 (16 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l5 (23 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l14 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l25 (22 kDa, Protein from Cutibacterium acnes)
- 23s ribosomal rna (1 MDa, RNA from Cutibacterium acnes)
- 50s ribosomal protein l32 (6 kDa, Protein from Cutibacterium acnes)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l4 (32 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l30 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l18 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l28 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l6 (19 kDa, Protein from Cutibacterium acnes)
- Water (18 Da, Ligand)
- 50s ribosomal protein l33 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l3 (23 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l2 (30 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l15 (15 kDa, Protein from Cutibacterium acnes)