Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 7ug7
Q-score: 0.536
Wieland M, Holm M, Rundlet EJ, Morici M, Koller TO, Maviza TP, Pogorevc D, Osterman IA, Muller R, Blanchard SC, Wilson DN
PNAS (2022) 119 pp. e2114214119-e2114214119 [ Pubmed: 35500116 DOI: doi:10.1073/pnas.2114214119 ]
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Argyrin b (874 Da, Protein from Actinoplanes sp.)
- 16s rrna (497 kDa, RNA from Escherichia coli)
- Elongation factor g (77 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 1,4-diaminobutane (88 Da, Ligand)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- Trna-fmet (24 kDa, RNA from Escherichia coli)
- Phenylalanine (165 Da, Ligand)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 70s ribosome in an intermediate state of translocation bound to ef-g(gdp) and argyrinb (2 MDa, Complex from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal subunit (Complex from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- Trna-phe (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- N-formylmethionine (177 Da, Ligand)
- Mrna (19 kDa, RNA from Escherichia coli)
- Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal subunit (Complex from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l1 (24 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7otc
Q-score: 0.504
Wieland M, Holm M, Rundlet EJ, Morici M, Koller TO, Maviza TP, Pogorevc D, Osterman IA, Muller R, Blanchard SC, Wilson DN
PNAS (2022) 119 pp. e2114214119-e2114214119 [ Pubmed: 35500116 DOI: doi:10.1073/pnas.2114214119 ]
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli BL21(DE3))
- Zinc ion (65 Da, Ligand)
- Elongation factor g (77 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s6 (12 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BL21(DE3))
- 1,4-diaminobutane (88 Da, Ligand)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BL21(DE3))
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli BL21(DE3))
- Cryo-em structure of an escherichia coli 70s ribosome in complex with elongation factor g and the antibiotic argyrinb (Complex from Escherichia coli BL21(DE3))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli BL21(DE3))
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli BL21(DE3))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s2 (25 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s7 (17 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli BL21(DE3))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BL21(DE3))
- Spermidine (145 Da, Ligand)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BL21(DE3))
- Argyrin b (838 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BL21(DE3))
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BL21(DE3))
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BL21(DE3))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BL21(DE3))
Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 7n1p
Q-score: 0.624
Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC
Nature (2021) 595 pp. 741-745 [ Pubmed: 34234344 DOI: doi:10.1038/s41586-021-03713-x ]
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 5s rrna (38 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 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 s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 16s rrna (499 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- Mrna (Complex from Escherichia coli BL21)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- Trna (24 kDa, RNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Spermidine (145 Da, Ligand)
- Water (18 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 23s rrna (941 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- Ribosome (Complex from Escherichia coli K-12)
- 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 l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- Mrna (19 kDa, RNA from Escherichia coli BL21)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- Trna molecules (Complex from Escherichia coli K-12)
- Ribosome (Complex)
- 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))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 50s ribosomal protein l28 (9 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 s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 1,4-diaminobutane (88 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 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))
- Chains: pp (425 Da, Protein from Escherichia coli K-12)
- Trna (24 kDa, RNA from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7n2c
Q-score: 0.533
Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC
Nature (2021) 595 pp. 741-745 [ Pubmed: 34234344 DOI: doi:10.1038/s41586-021-03713-x ]
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 5s rrna (38 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 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 s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 23s rrna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- Chains: pt (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s21 (8 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))
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- Trna (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- Elongation factor g (77 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 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 l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- Fusidic acid (516 Da, Ligand)
- 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))
- 50s ribosomal protein l1 (24 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli (strain K12))
- 16s rrna (497 kDa, RNA from Escherichia coli K-12)
- 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))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- Chains: mr (19 kDa, RNA from Escherichia coli K-12)
- Polypeptide (425 Da, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
- Elongating 70s ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to ef-g(gdp) (int2) (Complex from Escherichia coli K-12)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l7/l12 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
- 1,4-diaminobutane (88 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 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))
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
Elongating 70S ribosome complex in a hybrid-H1 pre-translocation (PRE-H1) conformation
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 7n2u
Q-score: 0.611
Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC
Nature (2021) 595 pp. 741-745 [ Pubmed: 34234344 DOI: doi:10.1038/s41586-021-03713-x ]
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 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 s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 5s rrna (38 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 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))
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- Ribosome (Complex from Escherichia coli K-12)
- 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 l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- Mrna (19 kDa, RNA from Escherichia coli BL21)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 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))
- 16s rrna (497 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- Trna (24 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Trna (24 kDa, RNA from Escherichia coli K-12)
- 23s rrna (941 kDa, RNA 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 s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 1,4-diaminobutane (88 Da, Ligand)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- Nascent peptide (425 Da, 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))
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 7n2v
Q-score: 0.572
Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC
Nature (2021) 595 pp. 741-745 [ DOI: doi:10.1038/s41586-021-03713-x Pubmed: 34234344 ]
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
- Elongating 70s ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to ef-g in an active, gtp conformation (int1) (Complex from Escherichia coli K-12)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli K-12)
- Elongation factor g (77 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
- Spectinomycin (332 Da, Ligand)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
- Trna (34 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
- Trna (34 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 1,4-diaminobutane (88 Da, Ligand)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Water (18 Da, Ligand)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli K-12)
- 5s rrna (38 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
- Nascent peptide (425 Da, Protein from Escherichia coli K-12)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
- 23s rrna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli K-12)
- Mrna (19 kDa, RNA from Escherichia coli BL21)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
- 16s rrna (497 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
Elongating 70S ribosome complex in a hybrid-H2* pre-translocation (PRE-H2*) conformation
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 7n30
Q-score: 0.592
Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC
Nature (2021) 595 pp. 741-745 [ Pubmed: 34234344 DOI: doi:10.1038/s41586-021-03713-x ]
- Elongating 70s ribosome complex in a hybrid-h2* pre-translocation (pre-h2*) conformation (Complex from Escherichia coli K-12)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 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 s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 5s rrna (38 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 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))
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 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 l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- Mrna (19 kDa, RNA from Escherichia coli BL21)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 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))
- 16s rrna (497 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- Trna (24 kDa, RNA from Escherichia coli K-12)
- 23s rrna (941 kDa, RNA 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 s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 1,4-diaminobutane (88 Da, Ligand)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- Nascent peptide (425 Da, 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))
- Trna (24 kDa, RNA from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
Elongating 70S ribosome complex in a post-translocation (POST) conformation
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 7n31
Q-score: 0.599
Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC
Nature (2021) 595 pp. 741-745 [ Pubmed: 34234344 DOI: doi:10.1038/s41586-021-03713-x ]
- 5s rrna (38 kDa, RNA from Escherichia coli K-12)
- Trna (24 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l31 (7 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)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
- Trna (24 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli K-12)
- Mrna (19 kDa, RNA from Escherichia coli BL21)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l25 (10 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)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 23s rrna (941 kDa, RNA from Escherichia coli K-12)
- Elongating 70s ribosome complex in a post-translocation (post) conformation (Complex from Escherichia coli K-12)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
- 16s rrna (497 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
- Polypeptide (425 Da, Protein from Escherichia coli K-12)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
- 1,4-diaminobutane (88 Da, Ligand)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)