› 8vy3

Electron Microscopy
2.98Å resolution

Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)

Released:
DOI: 10.2210/pdb8vy3/pdb
PDB entry 8vy3 coloured by chain, front view.
PDB entry 8vy3 coloured by chain, side view.
PDB entry 8vy3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.
Abe KM, Li G, He Q, Grant T, Lim CJ
Nat Commun 15 7705 (2024)
PMID: 39231985
Related structures: EMD-43628

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:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140801 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DNA primase small subunit Chain: A
Molecule details ›
Chain: A
Length: 412 amino acids
Theoretical weight: 49.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P49642 (Residues: 1-412; Coverage: 98%)
Gene name: PRIM1
Sequence domains: DNA primase small subunit
DNA primase large subunit Chain: B
Molecule details ›
Chain: B
Length: 434 amino acids
Theoretical weight: 50.54 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P49643 (Residues: 22-455; Coverage: 85%)
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: 1119 amino acids
Theoretical weight: 128.45 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P09884 (Residues: 338-1456; Coverage: 77%)
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: Trichoplusia ni
UniProt:
  • Canonical: Q14181 (Residues: 155-598; Coverage: 74%)
Gene name: POLA2
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.98Å
Relevant EMDB volumes: EMD-43628
Expression system: Trichoplusia ni

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