› 8fs4

Electron Microscopy
2.94Å resolution

Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 2 (open 9-1-1 ring and flexibly bound chamber DNA)

Released:
DOI: 10.2210/pdb8fs4/pdb
PDB entry 8fs4 coloured by chain, front view.
PDB entry 8fs4 coloured by chain, side view.
PDB entry 8fs4 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology.
Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H
OpenAccess logo bioRxiv (2023)
PMID: 37205533
Related structures: EMD-29413

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-234955 (preferred)
Entry contents:
8 distinct polypeptide molecules
3 distinct DNA molecules
Macromolecules (11 distinct):
Checkpoint protein RAD24 Chain: A
Molecule details ›
Chain: A
Length: 544 amino acids
Theoretical weight: 62.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32641 (Residues: 1-544; Coverage: 83%)
Gene names: RAD24, SYGP-ORF60, YER173W
Sequence domains: Rad17 P-loop domain
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: 336 amino acids
Theoretical weight: 37.84 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38629 (Residues: 1-336; Coverage: 99%)
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:
DNA damage checkpoint control protein MEC3 Chain: F
Molecule details ›
Chain: F
Length: 474 amino acids
Theoretical weight: 53.21 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02574 (Residues: 1-474; Coverage: 100%)
Gene names: L8003.15, MEC3, PIP3, PSO9, YLR288C
Sequence domains: Hus1-like protein
DNA damage checkpoint control protein RAD17 Chain: G
Molecule details ›
Chain: G
Length: 401 amino acids
Theoretical weight: 45.64 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P48581 (Residues: 1-401; Coverage: 100%)
Gene names: RAD17, YOR368W
Sequence domains: Repair protein Rad1/Rec1/Rad17
DNA damage checkpoint protein 1 Chain: H
Molecule details ›
Chain: H
Length: 612 amino acids
Theoretical weight: 69.79 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08949 (Residues: 1-612; Coverage: 100%)
Gene names: DDC1, YPL194W
Template strand Chain: I
Molecule details ›
Chain: I
Length: 50 nucleotides
Theoretical weight: 15.39 KDa
Primer strand 1 Chain: J
Molecule details ›
Chain: J
Length: 21 nucleotides
Theoretical weight: 6.46 KDa
Primer strand 2 Chain: K
Molecule details ›
Chain: K
Length: 20 nucleotides
Theoretical weight: 6.08 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.94Å
Relevant EMDB volumes: EMD-29413
Expression system: Saccharomyces cerevisiae

Quick links

Citations

2 mentions without citation

Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology.
Zheng et al. (2023)
1 more