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DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase

Electron Microscopy
14.06Å resolution
PDB entry 8v6i coloured by chain, front view.
PDB entry 8v6i coloured by chain, side view.
PDB entry 8v6i coloured by chain, top view.
Source organism: Xenopus laevis
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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Multimeric state: hetero hexamer
Accessible surface area: 113067.93 Å2
Buried surface area: 18072.36 Å2
Dissociation area: 1,208.05 Å2
Dissociation energy (ΔGdiss): 0.13 kcal/mol
Dissociation entropy (TΔSdiss): 15.3 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-236673

Macromolecules

DNA polymerase alpha catalytic subunit
Chain: A
Length: 1127 amino acids
Theoretical weight: 129.01 KDa
Source organism: Xenopus laevis
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9DE46 (Residues: 335-1458; Coverage: 77%)
Gene names: pola, pola1
Pfam:
DNA polymerase alpha catalytic subunit in PDB entry 8v6i, assembly 1, front view.
DNA polymerase alpha catalytic subunit in PDB entry 8v6i, assembly 1, side view.
DNA polymerase alpha catalytic subunit in PDB entry 8v6i, assembly 1, top view.
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DNA polymerase alpha subunit B
Chain: B
Length: 601 amino acids
Theoretical weight: 67.19 KDa
Source organism: Xenopus laevis
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q6DCZ1 (Residues: 1-598; Coverage: 100%)
Gene names: MGC80532, pola2, pola2.L
Pfam:
DNA polymerase alpha subunit B in PDB entry 8v6i, assembly 1, front view.
DNA polymerase alpha subunit B in PDB entry 8v6i, assembly 1, side view.
DNA polymerase alpha subunit B in PDB entry 8v6i, assembly 1, top view.
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DNA primase large subunit
Chain: C
Length: 513 amino acids
Theoretical weight: 59.67 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1L8G3G3 (Residues: 1-513; Coverage: 100%)
Gene name: prim2.S
Pfam: Eukaryotic and archaeal DNA primase, large subunit
DNA primase large subunit in PDB entry 8v6i, assembly 1, front view.
DNA primase large subunit in PDB entry 8v6i, assembly 1, side view.
DNA primase large subunit in PDB entry 8v6i, assembly 1, top view.
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DNA primase
Chain: D
Length: 423 amino acids
Theoretical weight: 49.36 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q800A4 (Residues: 1-420; Coverage: 100%)
Gene names: dnapol-alpha50, p49, prim1, prim1.S
Pfam: DNA primase small subunit
DNA primase in PDB entry 8v6i, assembly 1, front view.
DNA primase in PDB entry 8v6i, assembly 1, side view.
DNA primase in PDB entry 8v6i, assembly 1, top view.
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DNA chain E
Name: DNA template
Representative chains: E
Length: 50 nucleotides
Theoretical weight: 15.46 KDa
DNA template in PDB entry 8v6i, assembly 1, front view.
DNA template in PDB entry 8v6i, assembly 1, side view.
DNA template in PDB entry 8v6i, assembly 1, top view.
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DNA/RNA hybrid chain F
Name: RNA-DNA primer
Representative chains: F
Length: 20 nucleotides
Theoretical weight: 6.43 KDa
RNA-DNA primer in PDB entry 8v6i, assembly 1, front view.
RNA-DNA primer in PDB entry 8v6i, assembly 1, side view.
RNA-DNA primer in PDB entry 8v6i, assembly 1, top view.
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