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

Electron Microscopy
3.59Å resolution
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
Assembly composition:
hetero hexamer (preferred)
Entry contents: 4 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA polymerase alpha:primase complex and DNA
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Multimeric state: hetero hexamer
Accessible surface area: 115409.26 Å2
Buried surface area: 16686.97 Å2
Dissociation area: 1,119.98 Å2
Dissociation energy (ΔGdiss): -2.03 kcal/mol
Dissociation entropy (TΔSdiss): 15.24 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-216573

Macromolecules

DNA primase small subunit
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
Pfam: DNA primase small subunit
InterPro:
DNA primase small subunit in PDB entry 8d9d, assembly 1, front view.
DNA primase small subunit in PDB entry 8d9d, assembly 1, side view.
DNA primase small subunit in PDB entry 8d9d, assembly 1, top view.
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DNA primase large subunit
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
Pfam: Eukaryotic and archaeal DNA primase, large subunit
InterPro:
DNA primase large subunit in PDB entry 8d9d, assembly 1, front view.
DNA primase large subunit in PDB entry 8d9d, assembly 1, side view.
DNA primase large subunit in PDB entry 8d9d, assembly 1, top view.
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DNA polymerase alpha catalytic subunit
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
Pfam:
InterPro:
DNA polymerase alpha catalytic subunit in PDB entry 8d9d, assembly 1, front view.
DNA polymerase alpha catalytic subunit in PDB entry 8d9d, assembly 1, side view.
DNA polymerase alpha catalytic subunit in PDB entry 8d9d, assembly 1, top view.
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DNA polymerase alpha subunit B
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
Pfam:
InterPro:
DNA polymerase alpha subunit B in PDB entry 8d9d, assembly 1, front view.
DNA polymerase alpha subunit B in PDB entry 8d9d, assembly 1, side view.
DNA polymerase alpha subunit B in PDB entry 8d9d, assembly 1, top view.
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DNA chain F
Name: DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3')
Representative chains: F
Length: 19 nucleotides
Theoretical weight: 5.83 KDa
DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') in PDB entry 8d9d, assembly 1, front view.
DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') in PDB entry 8d9d, assembly 1, side view.
DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') in PDB entry 8d9d, assembly 1, top view.
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DNA/RNA hybrid chain E
Name: DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')
Representative chains: E
Length: 12 nucleotides
Theoretical weight: 3.98 KDa
DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') in PDB entry 8d9d, assembly 1, front view.
DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') in PDB entry 8d9d, assembly 1, side view.
DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') in PDB entry 8d9d, assembly 1, top view.
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