Cryo-EM structure of HflXr bound to the Listeria monocytogenes 50S ribosomal subunit.
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8a57
Q-score: 0.579
Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN
Nucleic Acids Res (2022) 50 pp. 11285-11300 [ DOI: doi:10.1093/nar/gkac934 Pubmed: 36300626 ]
- 50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 23s ribosomal rna (950 kDa, RNA from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- 50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
- Zinc ion (65 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
- Gtpase hflx (47 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
- 1,4-diaminobutane (88 Da, Ligand)
- Hflxr bound to the listeria monocytogenes 50s ribosomal subunit (1 MDa, Complex from Listeria monocytogenes E)
- 5s ribosomal rna (36 kDa, RNA from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l11 (14 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
Cryo-EM structure of Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8a5i
Q-score: 0.638
Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN
Nucleic Acids Res (2022) 50 pp. 11285-11300 [ DOI: doi:10.1093/nar/gkac934 Pubmed: 36300626 ]
- 50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 23s ribosomal rna (950 kDa, RNA from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- Lincomycin (406 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
- Potassium ion (39 Da, Ligand)
- Water (18 Da, Ligand)
- 50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
- Zinc ion (65 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- Lincomycin bound to the listeria monocytogenes 50s ribosomal subunit. (1 MDa, Complex from Listeria monocytogenes E)
- 50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
- 1,4-diaminobutane (88 Da, Ligand)
- 5s ribosomal rna (36 kDa, RNA from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit.
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a63
Q-score: 0.503
Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN
Nucleic Acids Res (2022) 50 pp. 11285-11300 [ Pubmed: 36300626 DOI: doi:10.1093/nar/gkac934 ]
- 50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- Spermidine (145 Da, Ligand)
- 50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 5s ribosomal rna (36 kDa, RNA from Listeria monocytogenes EGD-e)
- Zinc ion (65 Da, Ligand)
- Listeria monocytogenes 50s ribosomal subunit. (1 MDa, Complex from Listeria monocytogenes EGD-e)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
- 23s ribosomal rna (950 kDa, RNA from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
- 1,4-diaminobutane (88 Da, Ligand)
- 50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
- 50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ha1
Q-score: 0.48
Crowe-McAuliffe C, Graf M, Huter P, Takada H, Abdelshahid M, Novacek J, Murina V, Atkinson GC, Hauryliuk V, Wilson DN
PNAS (2018) 115 pp. 8978-8983 [ Pubmed: 30126986 DOI: doi:10.1073/pnas.1808535115 ]
- 50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis (strain 168))
- 16s ribosomal rna (503 kDa, RNA from Bacillus subtilis (strain 168))
- Trna (Complex from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis (strain 168))
- 70s ribosome (Complex from Bacillus subtilis (strain 168))
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis (strain 168))
- Telithromycin (812 Da, Ligand)
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis (strain 168))
- Ermd stalling peptide (Complex from Bacillus subtilis (strain 168))
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l27 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis (strain 168))
- P-trna (28 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 70s ribosome with p-trna translating the ermd stalling peptide and complexed with telithromycin (Complex)
- 50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis (strain 168))
- Mrna (872 Da, RNA from Bacillus subtilis (strain 168))
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis (strain 168))
- 5s ribosomal rna (36 kDa, RNA from Bacillus subtilis (strain 168))
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 23s ribosomal rna (949 kDa, RNA from Bacillus subtilis (strain 168))
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis (strain 168))
Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5l3p
Q-score: -0.001
Arenz S, Abdelshahid M, Sohmen D, Payoe R, Starosta AL, Berninghausen O, Hauryliuk V, Beckmann R, Wilson DN
Nucleic Acids Res (2016) 44 pp. 6471-6481 [ Pubmed: 27226493 DOI: doi:10.1093/nar/gkw470 ]
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- P-site trna (24 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- Deacylated a/r-trna (23 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- 16s ribosomal rna (498 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- Gtp pyrophosphokinase,gtp pyrophosphokinase,gtp pyrophosphokinase (90 kDa, Protein from Escherichia coli O157:H7)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli (strain K12))
- Cryo-em structure of stringent response factor rela bound to ermcl-stalled ribosome complex (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- Mrna (1 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))