Open state of RFC:PCNA bound to a 3' ss/dsDNA junction
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8dqx
Q-score: 0.621
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Dna (5'-d(p*tp*cp*cp*gp*ap*gp*cp*gp*ap*a)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Open state of rfc:pcna bound to a 3' ss/dsdna junction (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(*tp*tp*tp*tp*tp*t)-3') (1 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*gp*cp*cp*cp*gp*gp*a)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (29 kDa, Protein from Saccharomyces cerevisiae)
Intermediate state of RFC:PCNA bound to a 3' ss/dsDNA junction
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8dqz
Q-score: 0.47
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*cp*cp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Intermediate state of rfc:pcna bound to a 3' ss/dsdna junction (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*gp*gp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8dr0
Q-score: 0.575
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*cp*cp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*gp*gp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Closed state of rfc:pcna bound to a 3' ss/dsdna junction (Complex from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
Closed state of RFC:PCNA bound to a nicked dsDNA
Resolution: 2.39 Å
EM Method: Single-particle
Fitted PDBs: 8dr6
Q-score: 0.575
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Closed state of rfc:pcna bound to a nicked dsdna (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*a)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Dna (32-mer) (9 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Water (18 Da, Ligand)
Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8dqw
Q-score: 0.602
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Ddc1 isoform 1 (73 kDa, Protein from Saccharomyces cerevisiae)
- Dna (50-mer) (21 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*gp*tp*cp*cp*cp*tp*tp*cp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna damage checkpoint control protein rad17 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rad24 isoform 1 (80 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Water (18 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna damage checkpoint control protein mec3 (53 kDa, Protein from Saccharomyces cerevisiae)
- Open state of rad24-rfc:9-1-1 bound to a 5' ss/dsdna junction (Complex from Saccharomyces cerevisiae)
Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 8dr1
Q-score: 0.607
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Consensus closed state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*a)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Water (18 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*gp*gp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8dr3
Q-score: 0.59
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Closed state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) with ntd (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*a)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Water (18 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*gp*gp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
Resolution: 2.45 Å
EM Method: Single-particle
Fitted PDBs: 8dr4
Q-score: 0.555
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Open state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) without ntd (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*ap*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*gp*gp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8dr5
Q-score: 0.508
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Open state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) with ntd (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*c)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
Open state of RFC:PCNA bound to a nicked dsDNA
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8dr7
Q-score: 0.505
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ Pubmed: 35939393 DOI: doi:10.7554/eLife.78253 ]
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (26-mer) (7 kDa, DNA from Saccharomyces cerevisiae)
- Open state of rfc:pcna bound to a nicked dsdna (Complex from Saccharomyces cerevisiae)