Human polymerase epsilon bound to PCNA and DNA in the nucleotide bound state
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 9b8t
Q-score: 0.39
He Q, Wang F, Yao NY, O'Donnell ME, Li H
Nat Commun (2024) 15 pp. 7847-7847 [ DOI: doi:10.1038/s41467-024-52257-x Pubmed: 39245668 ]
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Template dna (18 kDa, DNA from DNA molecule)
- Primer dna (10 kDa, DNA from DNA molecule)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- The dna bound pol epsilon and pcna complex (450 kDa, Complex from Homo sapiens)
- Dna polymerase epsilon catalytic subunit (261 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8fs3
Q-score: 0.503
Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.03.539266 Pubmed: 37205533 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (37 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (15 kDa, DNA from synthetic construct)
- Rad24-rfc-911 clamp-dna (Complex)
- Primer strand 2 (6 kDa, DNA from synthetic construct)
- Checkpoint protein rad24 (62 kDa, Protein from Saccharomyces cerevisiae)
- Ddc1 isoform 1 (69 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein rad17 (45 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (Complex from synthetic construct)
- Dna damage checkpoint control protein mec3 (53 kDa, Protein from Saccharomyces cerevisiae)
- Proteins complex (Complex from Saccharomyces cerevisiae)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8fs4
Q-score: 0.452
Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.03.539266 Pubmed: 37205533 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (37 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (15 kDa, DNA from synthetic construct)
- Rad24-rfc-911 clamp-dna (Complex)
- Primer strand 2 (6 kDa, DNA from synthetic construct)
- Ddc1 isoform 1 (69 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein rad17 (45 kDa, Protein from Saccharomyces cerevisiae)
- Primer strand 1 (6 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (Complex from synthetic construct)
- Checkpoint protein rad24 (62 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein mec3 (53 kDa, Protein from Saccharomyces cerevisiae)
- Proteins complex (Complex from Saccharomyces cerevisiae)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8fs5
Q-score: 0.548
Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.03.539266 Pubmed: 37205533 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (37 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (15 kDa, DNA from synthetic construct)
- Rad24-rfc-911 clamp-dna (Complex)
- Primer strand 2 (6 kDa, DNA from synthetic construct)
- Checkpoint protein rad24 (62 kDa, Protein from Saccharomyces cerevisiae)
- Ddc1 isoform 1 (69 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein rad17 (45 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (Complex from synthetic construct)
- Primer strand 1 (6 kDa, DNA from synthetic construct)
- Dna damage checkpoint control protein mec3 (53 kDa, Protein from Saccharomyces cerevisiae)
- Proteins complex (Complex from Saccharomyces cerevisiae)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8fs6
Q-score: 0.487
Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.03.539266 Pubmed: 37205533 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (37 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (15 kDa, DNA from synthetic construct)
- Rad24-rfc-911 clamp-dna (Complex)
- Primer strand 2 (6 kDa, DNA from synthetic construct)
- Checkpoint protein rad24 (62 kDa, Protein from Saccharomyces cerevisiae)
- Ddc1 isoform 1 (69 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein rad17 (45 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (Complex from synthetic construct)
- Primer strand 1 (6 kDa, DNA from synthetic construct)
- Dna damage checkpoint control protein mec3 (53 kDa, Protein from Saccharomyces cerevisiae)
- Proteins complex (Complex from Saccharomyces cerevisiae)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8fs7
Q-score: 0.542
Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.03.539266 Pubmed: 37205533 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (37 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (15 kDa, DNA from synthetic construct)
- Rad24-rfc-911 clamp-dna (Complex)
- Primer strand 2 (6 kDa, DNA from synthetic construct)
- Checkpoint protein rad24 (62 kDa, Protein from Saccharomyces cerevisiae)
- Ddc1 isoform 1 (69 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein rad17 (45 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (Complex from synthetic construct)
- Primer strand 1 (6 kDa, DNA from synthetic construct)
- Dna damage checkpoint control protein mec3 (53 kDa, Protein from Saccharomyces cerevisiae)
- Proteins complex (Complex from Saccharomyces cerevisiae)