› 5xs0

X-ray diffraction
3Å resolution

Structure of a ssDNA bound to the outer DNA binding site of RAD52

Released:
DOI: 10.2210/pdb5xs0/pdb
PDB entry 5xs0 coloured by chain, front view.
PDB entry 5xs0 coloured by chain, side view.
PDB entry 5xs0 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of Homology-Directed DNA Repair Mediated by RAD52.
Saotome M, Saito K, Yasuda T, Ohtomo H, Sugiyama S, Nishimura Y, Kurumizaka H, Kagawa W
iScience 3 50-62 (2018)
PMID: 30428330

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218996 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
DNA repair protein RAD52 homolog Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
Length: 215 amino acids
Theoretical weight: 23.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P43351 (Residues: 1-212; Coverage: 51%)
Gene name: RAD52
Sequence domains: Rad52/22 family double-strand break repair protein
Structure domains: DNA repair protein Rad52/59/22
ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3') Chain: W
Molecule details ›
Chain: W
Length: 6 nucleotides
Theoretical weight: 1.69 KDa
Source organism: synthetic construct
Expression system: Not provided
ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3') Chain: X
Molecule details ›
Chain: X
Length: 8 nucleotides
Theoretical weight: 2.27 KDa
Source organism: synthetic construct
Expression system: Not provided
ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') Chain: Y
Molecule details ›
Chain: Y
Length: 10 nucleotides
Theoretical weight: 2.85 KDa
Source organism: synthetic construct
Expression system: Not provided
ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') Chain: Z
Molecule details ›
Chain: Z
Length: 9 nucleotides
Theoretical weight: 2.56 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 100.224Å b: 164.408Å c: 166.087Å
α: 90° β: 90.19° γ: 90°
R-values:
R R work R free
0.222 0.221 0.251
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

RAD52: Paradigm of Synthetic Lethality and New Developments.
Rossi et al. (2021)
6 more

6 mentions without citation

Structure and mechanism of the Red recombination system of bacteriophage λ.
Caldwell et al. (2019)
5 more