› 4fyd

X-ray diffraction
3.1Å resolution

Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP

Released:
DOI: 10.2210/pdb4fyd/pdb
PDB entry 4fyd coloured by chain, front view.
PDB entry 4fyd coloured by chain, side view.
PDB entry 4fyd coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Mechanism for priming DNA synthesis by yeast DNA polymerase α.
Perera RL, Torella R, Klinge S, Kilkenny ML, Maman JD, Pellegrini L
Elife 2 e00482 (2013)
PMID: 23599895

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-113148 (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 A Chains: A, B
Molecule details ›
Chains: A, B
Length: 910 amino acids
Theoretical weight: 103.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13382 (Residues: 349-1258; Coverage: 62%)
Gene names: CDC17, N2181, POL1, YNL102W
Sequence domains:
Structure domains:
DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 25 nucleotides
Theoretical weight: 7.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 12 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand DGT 2 x DGT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 111.689Å b: 145.686Å c: 197.199Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

Eukaryotic DNA Replication Fork.
Burgers et al. (2017)
12 more

8 mentions without citation

Structural insights into eukaryotic DNA replication.
Doublié et al. (2014)
7 more