RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ope
Q-score: 0.309
Takada H, Crowe-McAuliffe C, Polte C, Sidorova ZY, Murina V, Atkinson GC, Konevega AL, Ignatova Z, Wilson DN, Hauryliuk V
Nucleic Acids Res (2021) 49 pp. 8355-8369 [ Pubmed: 34255840 DOI: doi:10.1093/nar/gkab589 ]
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Trna-ala-ugc (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 5s rrna (38 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l10 (18 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- Rqc complex consisting of 50s large ribosomal subunit, peptidyl-trna, rqcp, and dr-variant rqch (Complex)
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rqc2 homolog rqch (68 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Uncharacterized protein yabo (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l11 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7asa
Q-score: 0.405
Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V
Mol Cell (2021) 81 pp. 115- [ DOI: doi:10.1016/j.molcel.2020.11.002 Pubmed: 33259810 ]
- Rqch (Complex from Bacillus subtilis (strain 168))
- Trna-ala-1-1 (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- Uncharacterized protein yabo (9 kDa, Protein from Bacillus subtilis (strain 168))
- P-trna, and yabo/rqcp (Complex from Bacillus subtilis (strain 168))
- Rqc2 homolog rqch (68 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal subunit in complex with rqch, p-trna, and yabo/rqcp (1 MDa, Complex)
- 50s ribosomal protein l11 (14 kDa, Protein from Bacillus subtilis (strain 168))
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7as8
Q-score: 0.497
Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V
Mol Cell (2021) 81 pp. 115- [ DOI: doi:10.1016/j.molcel.2020.11.002 Pubmed: 33259810 ]
- Trna-ala-1-1 (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l10 (18 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 5s rrna (38 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis (strain 168))
- Uncharacterized protein yabo (9 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l27 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal subunit in complex with p-trna, and yabo/rqcp (Complex from Bacillus subtilis (strain 168))
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis (strain 168))
- Rqc2 homolog rqch (68 kDa, Protein from Bacillus subtilis (strain 168))
- Rqch (Complex from Bacillus subtilis (strain 168))
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l11 (14 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis (strain 168))
- 23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal subunit in complex with rqch, p-trna, and yabo/rqcp (1 MDa, Complex)
Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 6szs
Q-score: 0.535
Shimokawa-Chiba N, Muller C, Fujiwara K, Beckert B, Ito K, Wilson DN, Chiba S
Nat Commun (2019) 10 pp. 5397-5397 [ DOI: doi:10.1038/s41467-019-13408-7 Pubmed: 31776341 ]
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli ribosome with p-site trna-pro(cgg, carrying the nascent chain (Complex from Escherichia coli K-12)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- Mrna (1 kDa, RNA from Escherichia coli K-12)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- Uncharacterized protein yqkk (8 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli (strain K12))
- Bacillus subtilis ribosome rescue factor (brfa; former yqkk) and peptide chain release factor 2 (rf2) (Complex from Bacillus subtilis (strain 168))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
- P-site trna-pro(cgg) (24 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- E. coli 70s stalled on truncated mrna in complex bsbrfa and bsrf2-q251p (Complex)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli (strain K12))
- Peptide chain release factor 2 (41 kDa, Protein from Bacillus subtilis (strain 168))