› 8dr4

Electron Microscopy
2.45Å resolution

Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD

Released:
DOI: 10.2210/pdb8dr4/pdb
PDB entry 8dr4 coloured by chain, front view.
PDB entry 8dr4 coloured by chain, side view.
PDB entry 8dr4 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Multistep loading of a DNA sliding clamp onto DNA by replication factor C.
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
OpenAccess logo Elife 11 (2022)
PMID: 35939393
Related structures: EMD-27670

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122520 (preferred)
Entry contents:
6 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (10 distinct):
Replication factor C subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 918 amino acids
Theoretical weight: 101.69 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38630 (Residues: 1-861; Coverage: 100%)
Gene names: CDC44, RFC1, YOR217W, YOR50-7
Sequence domains:
Replication factor C subunit 4 Chain: B
Molecule details ›
Chain: B
Length: 323 amino acids
Theoretical weight: 36.2 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40339 (Residues: 1-323; Coverage: 100%)
Gene names: O0923, RFC4, YOL094C
Sequence domains:
Replication factor C subunit 3 Chain: C
Molecule details ›
Chain: C
Length: 340 amino acids
Theoretical weight: 38.25 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38629 (Residues: 1-340; Coverage: 100%)
Gene names: N0533, RFC3, YNL290W
Sequence domains:
Replication factor C subunit 2 Chain: D
Molecule details ›
Chain: D
Length: 353 amino acids
Theoretical weight: 39.79 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40348 (Residues: 1-353; Coverage: 100%)
Gene names: J1808, RFC2, YJR068W
Sequence domains:
Replication factor C subunit 5 Chain: E
Molecule details ›
Chain: E
Length: 354 amino acids
Theoretical weight: 39.99 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38251 (Residues: 1-354; Coverage: 100%)
Gene names: RFC5, YBR0810, YBR087W
Sequence domains:
Proliferating cell nuclear antigen Chains: F, G, H
Molecule details ›
Chains: F, G, H
Length: 277 amino acids
Theoretical weight: 30.99 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P15873 (Residues: 1-258; Coverage: 100%)
Gene names: POL30, YBR0811, YBR088C
Sequence domains:
DNA (5'-D(P*TP*TP*TP*CP*GP*GP*GP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*GP*G)-3') Chain: I
Molecule details ›
Chain: I
Length: 19 nucleotides
Theoretical weight: 6.01 KDa
DNA (5'-D(P*CP*CP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*CP*CP*CP*GP*GP*C)-3') Chain: J
Molecule details ›
Chain: J
Length: 18 nucleotides
Theoretical weight: 5.32 KDa
DNA (5'-D(P*AP*AP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') Chain: K
Molecule details ›
Chain: K
Length: 12 nucleotides
Theoretical weight: 3.87 KDa
DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*TP*TP*T)-3') Chain: L
Molecule details ›
Chain: L
Length: 13 nucleotides
Theoretical weight: 3.76 KDa

Ligands and Environments

3 bound ligands:
Ligand AGS 4 x AGS
Ligand MG 4 x MG
Ligand GDP 1 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.45Å
Relevant EMDB volumes: EMD-27670
Expression system: Saccharomyces cerevisiae

Quick links

Citations

5 citation in other articles

Unexpected new insights into DNA clamp loaders: Eukaryotic clamp loaders contain a second DNA site for recessed 5' ends that facilitates repair and signals DNA damage: Eukaryotic clamp loaders contain a second DNA site for recessed 5' ends that facilitates repair and signals DNA damage.
Li et al. (2022)
4 more

1 mention without citation

Multistep loading of a DNA sliding clamp onto DNA by replication factor C.
Schrecker et al. (2022)