› 7jl8

X-ray diffraction
2.1Å resolution

Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion

Released:
DOI: 10.2210/pdb7jl8/pdb
PDB entry 7jl8 coloured by chain, front view.
PDB entry 7jl8 coloured by chain, side view.
PDB entry 7jl8 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.
Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK
OpenAccess logo Nat Commun 12 4020 (2021)
PMID: 34188055

Function and Biology Details

Reactions catalysed: 
SsDNA + n NTP = ssDNA/pppN(pN)(n-1) hybrid + (n-1) diphosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121356 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed primase/polymerase protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 354 amino acids
Theoretical weight: 41.04 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q96LW4 (Residues: 1-354; Coverage: 63%)
Gene names: CCDC111, PRIMPOL
Sequence domains: DNA primase small subunit
DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3') Chains: C, G
Molecule details ›
Chains: C, G
Length: 17 nucleotides
Theoretical weight: 5.05 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 3 x CA
Ligand GOL 5 x GOL
Ligand EDO 1 x EDO
Ligand PEG 3 x PEG
1 modified residue:
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 50.689Å b: 65.33Å c: 72.001Å
α: 68.47° β: 85.67° γ: 86.92°
R-values:
R R work R free
0.188 0.187 0.213
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

4 review citations

Roles for the 8-Oxoguanine DNA Repair System in Protecting Telomeres From Oxidative Stress.
De Rosa et al. (2021)
3 more

2 mentions without citation

Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.
Rechkoblit et al. (2021)
1 more