› 4yir

X-ray diffraction
3.05Å resolution

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA

Released:
DOI: 10.2210/pdb4yir/pdb
PDB entry 4yir coloured by chain, front view.
PDB entry 4yir coloured by chain, side view.
PDB entry 4yir coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.
Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH
Nat Commun 6 5849 (2015)
PMID: 25562780

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118320 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA repair protein RAD4 Chain: A
Molecule details ›
Chain: A
Length: 538 amino acids
Theoretical weight: 62.59 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P14736 (Residues: 101-632; Coverage: 71%)
Gene names: RAD4, YER162C
Sequence domains:
Structure domains:
UV excision repair protein RAD23 Chain: X
Molecule details ›
Chain: X
Length: 171 amino acids
Theoretical weight: 17.78 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32628 (Residues: 230-398; Coverage: 43%)
Gene names: RAD23, SYGP-ORF29, YEL037C
Sequence domains:
Structure domains: XPC-binding domain
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3') Chain: W
Molecule details ›
Chain: W
Length: 24 nucleotides
Theoretical weight: 7.29 KDa
DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3') Chain: Y
Molecule details ›
Chain: Y
Length: 24 nucleotides
Theoretical weight: 7.51 KDa

Ligands and Environments

No bound ligands
1 modified residue:
Ligand G47 1 x G47

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P41212
Unit cell:
a: 79.405Å b: 79.405Å c: 404.366Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.192 0.253
Expression system: Trichoplusia ni

Quick links

Citations

13 review citations

Molecular mechanisms of DNA damage recognition for mammalian nucleotide excision repair.
Sugasawa K. (2016)
12 more

6 mentions without citation

Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly.
Fadda E. (2016)
5 more