7rbj

X-ray diffraction
1.91Å resolution

Human DNA polymerase beta crosslinked complex, 30 s Ca to Mg exchange

Released:
Model geometry
Fit model/data
Primary publication:
Interlocking activities of DNA polymerase β in the base excision repair pathway.
OpenAccess logo Proc Natl Acad Sci U S A 119 e2118940119 (2022)
PMID: 35238634

Function and Biology Details

Reactions catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-121897 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 39.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Sequence domains:
DNA (5'-D(*GP*TP*CP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') Chain: P
DNA (5'-D(P*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: T

Ligands and Environments

No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 50.794Å b: 80.841Å c: 55.716Å
α: 90° β: 107.79° γ: 90°
R-values:
R R work R free
0.19 0.188 0.229
Expression systems:
  • Escherichia coli
  • Not provided