› 4qcl

X-ray diffraction
2.2Å resolution

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dCTP

Released:
DOI: 10.2210/pdb4qcl/pdb
PDB entry 4qcl coloured by chain, front view.
PDB entry 4qcl coloured by chain, side view.
PDB entry 4qcl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Activity and fidelity of human DNA polymerase alpha depend on primer structure
Baranovskiy AG, Duong V, Babayeva ND, Zhang Y, Pavlov Y, Anderson K, Tahirov TH
J. Biol. Chem. (2018)

Function and Biology Details

Reaction catalysed: 
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-113164 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
DNA polymerase alpha catalytic subunit Chain: A
Molecule details ›
Chain: A
Length: 922 amino acids
Theoretical weight: 105.58 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P09884 (Residues: 336-1257; Coverage: 63%)
Gene names: POLA, POLA1
Sequence domains:
Structure domains:
DNA TEMPLATE Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA PRIMER Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.52 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand DCP 1 x DCP
Ligand MG 1 x MG
Ligand ZN 3 x ZN
Ligand K 1 x K
Ligand 1PE 1 x 1PE
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P3221
Unit cell:
a: 140.763Å b: 140.763Å c: 181.315Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.21 0.239
Expression systems:
  • Spodoptera frugiperda
  • Not provided

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