› 5l2x

X-ray diffraction
2.2Å resolution

Crystal structure of human PrimPol ternary complex

Released:
DOI: 10.2210/pdb5l2x/pdb
PDB entry 5l2x coloured by chain, front view.
PDB entry 5l2x coloured by chain, side view.
PDB entry 5l2x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and mechanism of human PrimPol, a DNA polymerase with primase activity.
Rechkoblit O, Gupta YK, Malik R, Rajashankar KR, Johnson RE, Prakash L, Prakash S, Aggarwal AK
Sci Adv 2 e1601317 (2016)
PMID: 27819052

Function and Biology Details

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-118979 (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: 353 amino acids
Theoretical weight: 40.91 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q96LW4 (Residues: 1-353; Coverage: 63%)
Gene names: CCDC111, PRIMPOL
Sequence domains: DNA primase small subunit
DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3') Chains: C, G
Molecule details ›
Chains: C, G
Length: 17 nucleotides
Theoretical weight: 5.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 13 nucleotides
Theoretical weight: 4.09 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 2 x CA
2 modified residues:
Ligand 5IU 2 x 5IU
Ligand DDG 2 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 50.723Å b: 65.212Å c: 72.463Å
α: 67.89° β: 85.22° γ: 86.65°
R-values:
R R work R free
0.208 0.206 0.255
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

14 review citations

PrimPol-Prime Time to Reprime.
Guilliam et al. (2017)
13 more

13 mentions without citation

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism.
Yang et al. (2018)
12 more