Damaged 70S ribosome with PrfH bound
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 9mor
Q-score: 0.367
Tian Y, Li Q, Fatma S, Jiang J, Jin H, Zeng F, Huang RH
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.09.632186 Pubmed: 39829893 ]
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- Putative peptide chain release factor homolog (Cellular component)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- P-trna, e-trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Damaged 70s with prfh (Complex from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 30s (Complex)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Peptide chain release factor h (26 kDa, Protein from Capnocytophaga gingivalis)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli)
- Trna (Cellular component)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Mrna (8 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s (Complex)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Damaged 70S ribosome with PrfH bound
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 9mq4
Q-score: 0.462
Tian Y, Li Q, Fatma S, Jiang J, Jin H, Zeng F, Huang RH
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.09.632186 Pubmed: 39829893 ]
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- Putative peptide chain release factor homolog (Cellular component)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- P-trna, e-trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Damaged 70s with prfh (Complex from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli 0.1197)
- 30s (Complex)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Trna (Cellular component)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Mrna (8 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s (Complex)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Peptide chain release factor h (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Structure of the human endogenous PCNA-FEN1 complex - State A
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8yjh
Q-score: 0.421
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Endogenous state a pcna-dna-fen1 complex (Complex from Homo sapiens)
- Upstream dna chain j (4 kDa, DNA from Homo sapiens)
- Downstream dna chain f (3 kDa, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Parent strand chain e (7 kDa, DNA from Homo sapiens)
- 5 prime dna (867 Da, DNA from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State B
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8yjl
Q-score: 0.448
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Parent strand (8 kDa, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Upstream dna (5 kDa, DNA from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Endogenous state b pcna-dna-fen1 complex (Complex from Homo sapiens)
- 5 prime dna (867 Da, DNA from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State C
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8yjq
Q-score: 0.441
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Endogenous state c pcna-dna-fen1 complex (Complex from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- 5 prime flap dna (1 kDa, DNA from Homo sapiens)
- Upstream dna (5 kDa, DNA from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sapiens)
- Parent strand (8 kDa, DNA from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State D
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8yjr
Q-score: 0.423
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Upstream dna (6 kDa, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- 5 prime flap dna (867 Da, DNA from Homo sapiens)
- Endogenous state d pcna-dna-fen1 complex (Complex from Homo sapiens)
- Parent dna (9 kDa, DNA from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State E
Resolution: 3.55 Å
EM Method: Single-particle
Fitted PDBs: 8yjs
Q-score: 0.443
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Endogenous state e pcna-dna-fen1 complex (Complex from Homo sapiens)
- 5 prime flap dna (867 Da, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sapiens)
- Upstream dna (5 kDa, DNA from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Parent strand dna (8 kDa, DNA from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State F
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 8yju
Q-score: 0.399
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Parent strand dna (9 kDa, DNA from Homo sapiens)
- Upstream dna (6 kDa, DNA from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Endogenous state f pcna-dna-fen1 complex (Complex from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- 5 prime flap dna (867 Da, DNA from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State G
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8yjv
Q-score: 0.447
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Upstream dna (6 kDa, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Endogenous state g pcna-dna-fen1 complex (Complex from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sa)
- Parent strand dna (9 kDa, DNA from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- 5 prime flap dna (867 Da, DNA from Homo sapiens)
Structure of the human endogenous PCNA-FEN1 complex - State H
EMBO J (2025) 44 pp. 484-504 [ DOI: doi:10.1038/s44318-024-00296-x Pubmed: 39578540 ]
- Parent strand dna (9 kDa, DNA from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Downstream dna (3 kDa, DNA from Homo sapiens)
- Upstream dna (6 kDa, DNA from Homo sapiens)
- Endogenous state h pcna-dna-fen1 complex (Complex from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- 5 prime flap dna (867 Da, DNA from Homo sapiens)