› 8d9d

Electron Microscopy
3.59Å resolution

Human DNA polymerase-alpha/primase elongation complex II bound to primer/template

Released:
DOI: 10.2210/pdb8d9d/pdb
PDB entry 8d9d coloured by chain, front view.
PDB entry 8d9d coloured by chain, side view.
PDB entry 8d9d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of human primosome elongation complexes.
He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH
Nat Struct Mol Biol (2023)
PMID: 37069376
Related structures: EMD-27258

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-216573 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (6 distinct):
DNA primase small subunit Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 49.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P49642 (Residues: 1-420; Coverage: 100%)
Gene name: PRIM1
Sequence domains: DNA primase small subunit
DNA primase large subunit Chain: B
Molecule details ›
Chain: B
Length: 509 amino acids
Theoretical weight: 58.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P49643 (Residues: 1-509; Coverage: 100%)
Gene names: PRIM2, PRIM2A
Sequence domains: Eukaryotic and archaeal DNA primase, large subunit
DNA polymerase alpha catalytic subunit Chain: C
Molecule details ›
Chain: C
Length: 1462 amino acids
Theoretical weight: 166.13 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P09884 (Residues: 1-1462; Coverage: 100%)
Gene names: POLA, POLA1
Sequence domains:
DNA polymerase alpha subunit B Chain: D
Molecule details ›
Chain: D
Length: 444 amino acids
Theoretical weight: 49.07 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q14181 (Residues: 155-598; Coverage: 74%)
Gene name: POLA2
Sequence domains:
DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 19 nucleotides
Theoretical weight: 5.83 KDa
DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 12 nucleotides
Theoretical weight: 3.98 KDa

Ligands and Environments

4 bound ligands:
Ligand ZN 3 x ZN
Ligand SF4 1 x SF4
Ligand MG 2 x MG
Ligand DTP 1 x DTP
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.59Å
Relevant EMDB volumes: EMD-27258
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Spodoptera frugiperda

Quick links

Citations

2 review citations

Models for human telomere C-strand fill-in by CST-PolĪ±-primase.
He et al. (2023)
1 more

2 mentions without citation

Structures of human primosome elongation complexes.
He et al. (2023)
1 more