Rnase R bound to a 30S degradation intermediate (main state)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8cdu
Q-score: 0.468
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (state II)
Resolution: 4.73 Å
EM Method: Single-particle
Fitted PDBs: 8cdv
Q-score: 0.272
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (3 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8cec
Q-score: 0.388
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribonuclease r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Resolution: 4.15 Å
EM Method: Single-particle
Fitted PDBs: 8ced
Q-score: 0.265
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rnase r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8cee
Q-score: 0.298
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
Nature (2024) 626 pp. 1133-1140 [ Pubmed: 38326618 DOI: doi:10.1038/s41586-024-07027-6 ]
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (28 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rna substrate (2 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (24 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Rnase r (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal subunit in complex with 3' exonuclease rnase r (Complex from Bacillus subtilis subsp. subtilis str. 168)