› 8vfa

X-ray diffraction
2.05Å resolution

Ternary DNA Polymerase Beta bound to DNA containing primer terminal dC base-paired with FapydG

Released:
DOI: 10.2210/pdb8vfa/pdb
PDB entry 8vfa coloured by chain, front view.
PDB entry 8vfa coloured by chain, side view.
PDB entry 8vfa coloured by chain, top view.
Source organisms:
Primary publication:
Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase β.
Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM
OpenAccess logo Nucleic Acids Res (2024)
PMID: 38634780

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
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-513375 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 38.24 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(*CP*CP*GP*AP*CP*CP*(FAP)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.85 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*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

Ligands and Environments

3 bound ligands:
Ligand G2P 1 x G2P
Ligand NA 2 x NA
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 54.437Å b: 79.531Å c: 54.889Å
α: 90° β: 108.26° γ: 90°
R-values:
R R work R free
0.229 0.226 0.267
Expression systems:
  • Escherichia coli
  • Not provided

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