› 6uin

X-ray diffraction
3.35Å resolution

Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

Released:
DOI: 10.2210/pdb6uin/pdb
PDB entry 6uin coloured by chain, front view.
PDB entry 6uin coloured by chain, side view.
PDB entry 6uin coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Tethering-facilitated DNA 'opening' and complementary roles of beta-hairpin motifs in the Rad4/XPC DNA damage sensor protein
Paul D, Mu H, Tavakoli A, Dai Q, Chen X, Chakraborty S, He C, Ansari A, Broyde S, Min JH
Nucleic Acids Res. 48 12348-12364 (2021)

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-120698 (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: 62.56 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P14736 (Residues: 101-632; Coverage: 71%)
Gene names: RAD4, YER162C
Sequence 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
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32628 (Residues: 230-398; Coverage: 43%)
Gene names: RAD23, SYGP-ORF29, YEL037C
Sequence domains:
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3') Chain: W
Molecule details ›
Chain: W
Length: 24 nucleotides
Theoretical weight: 7.25 KDa
DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*NP*NP*NP*NP*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: 7.01 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: P65
Unit cell:
a: 77.665Å b: 77.665Å c: 264.054Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.214 0.209 0.262
Expression system: Trichoplusia ni

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