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Human polymerase delta holoenzyme Conformer 2

Electron Microscopy
4.86Å resolution
PDB entry 6s1n coloured by chain, front view.
PDB entry 6s1n coloured by chain, side view.
PDB entry 6s1n coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero nonamer (preferred)
Entry contents: 5 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: PCNA homotrimer and DNA
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Multimeric state: hetero nonamer
Accessible surface area: 115217.8 Å2
Buried surface area: 24703.92 Å2
Dissociation area: 1,781.73 Å2
Dissociation energy (ΔGdiss): -7.74 kcal/mol
Dissociation entropy (TΔSdiss): 28.26 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120594

Macromolecules

DNA polymerase delta catalytic subunit
Chain: A
Length: 1107 amino acids
Theoretical weight: 123.79 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P28340 (Residues: 1-1107; Coverage: 100%)
Gene names: POLD, POLD1
Pfam:
InterPro:
DNA polymerase delta catalytic subunit in PDB entry 6s1n, assembly 1, front view.
DNA polymerase delta catalytic subunit in PDB entry 6s1n, assembly 1, side view.
DNA polymerase delta catalytic subunit in PDB entry 6s1n, assembly 1, top view.
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DNA polymerase delta subunit 2
Chain: B
Length: 469 amino acids
Theoretical weight: 51.34 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P49005 (Residues: 1-469; Coverage: 100%)
Gene name: POLD2
Pfam:
InterPro:
DNA polymerase delta subunit 2 in PDB entry 6s1n, assembly 1, front view.
DNA polymerase delta subunit 2 in PDB entry 6s1n, assembly 1, side view.
DNA polymerase delta subunit 2 in PDB entry 6s1n, assembly 1, top view.
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DNA polymerase delta subunit 3
Chain: C
Length: 474 amino acids
Theoretical weight: 52.53 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q15054 (Residues: 2-466; Coverage: 100%)
Gene names: KIAA0039, POLD3
Pfam: DNA polymerase subunit Cdc27
InterPro:
DNA polymerase delta subunit 3 in PDB entry 6s1n, assembly 1, front view.
DNA polymerase delta subunit 3 in PDB entry 6s1n, assembly 1, side view.
DNA polymerase delta subunit 3 in PDB entry 6s1n, assembly 1, top view.
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DNA polymerase delta subunit 4
Chain: D
Length: 137 amino acids
Theoretical weight: 16.27 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9HCU8 (Residues: 2-107; Coverage: 99%)
Gene names: POLD4, POLDS
Pfam: DNA polymerase delta, subunit 4
InterPro: DNA polymerase delta, subunit 4
DNA polymerase delta subunit 4 in PDB entry 6s1n, assembly 1, front view.
DNA polymerase delta subunit 4 in PDB entry 6s1n, assembly 1, side view.
DNA polymerase delta subunit 4 in PDB entry 6s1n, assembly 1, top view.
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Proliferating cell nuclear antigen
Chains: E, F, G
Length: 264 amino acids
Theoretical weight: 29.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12004 (Residues: 1-261; Coverage: 100%)
Gene name: PCNA
Pfam:
InterPro:
Proliferating cell nuclear antigen in PDB entry 6s1n, assembly 1, front view.
Proliferating cell nuclear antigen in PDB entry 6s1n, assembly 1, side view.
Proliferating cell nuclear antigen in PDB entry 6s1n, assembly 1, top view.
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DNA chain P
Name: DNA primer
Representative chains: P
Length: 25 nucleotides
Theoretical weight: 7.67 KDa
DNA primer in PDB entry 6s1n, assembly 1, front view.
DNA primer in PDB entry 6s1n, assembly 1, side view.
DNA primer in PDB entry 6s1n, assembly 1, top view.
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DNA chain T
Name: DNA template
Representative chains: T
Length: 38 nucleotides
Theoretical weight: 11.68 KDa
DNA template in PDB entry 6s1n, assembly 1, front view.
DNA template in PDB entry 6s1n, assembly 1, side view.
DNA template in PDB entry 6s1n, assembly 1, top view.
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