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Archaeal DNA ligase and heterotrimeric PCNA in complex with non-ligatable DNA

Electron Microscopy
4.16Å resolution
PDB entry 7rpo coloured by chain, front view.
PDB entry 7rpo coloured by chain, side view.
PDB entry 7rpo coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Assembly composition:
hetero heptamer (preferred)
Entry contents: 4 distinct polypeptide molecules
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero heptamer
Accessible surface area: 68439.98 Å2
Buried surface area: 13360.21 Å2
Dissociation area: 2,054.33 Å2
Dissociation energy (ΔGdiss): 3.3 kcal/mol
Dissociation entropy (TΔSdiss): 27.93 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-121928

Macromolecules

DNA polymerase sliding clamp 1
Chain: A
Length: 258 amino acids
Theoretical weight: 28.71 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: P57766 (Residues: 2-249; Coverage: 100%)
Gene names: C41_008, SSO0397, pcn1, pcnA-like
Pfam: Proliferating cell nuclear antigen, N-terminal domain
InterPro:
DNA polymerase sliding clamp 1 in PDB entry 7rpo, assembly 1, front view.
DNA polymerase sliding clamp 1 in PDB entry 7rpo, assembly 1, side view.
DNA polymerase sliding clamp 1 in PDB entry 7rpo, assembly 1, top view.
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DNA polymerase sliding clamp 2
Chain: B
Length: 245 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97Z84 (Residues: 1-245; Coverage: 100%)
Gene names: SSO1047, pcn2, pcnA-2
Pfam:
InterPro:
DNA polymerase sliding clamp 2 in PDB entry 7rpo, assembly 1, front view.
DNA polymerase sliding clamp 2 in PDB entry 7rpo, assembly 1, side view.
DNA polymerase sliding clamp 2 in PDB entry 7rpo, assembly 1, top view.
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DNA polymerase sliding clamp 3
Chain: C
Length: 252 amino acids
Theoretical weight: 28.56 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: P57765 (Residues: 1-244; Coverage: 100%)
Gene names: C41_016, SSO0405, pcn3, pcnA-1
Pfam:
InterPro:
DNA polymerase sliding clamp 3 in PDB entry 7rpo, assembly 1, front view.
DNA polymerase sliding clamp 3 in PDB entry 7rpo, assembly 1, side view.
DNA polymerase sliding clamp 3 in PDB entry 7rpo, assembly 1, top view.
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DNA ligase
Chain: E
Length: 621 amino acids
Theoretical weight: 70 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q980T8 (Residues: 1-601; Coverage: 100%)
Gene names: SSO0189, lig
Pfam:
InterPro:
DNA ligase in PDB entry 7rpo, assembly 1, front view.
DNA ligase in PDB entry 7rpo, assembly 1, side view.
DNA ligase in PDB entry 7rpo, assembly 1, top view.
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DNA chain X
Name: Upstream strand DNA
Representative chains: X
Length: 24 nucleotides
Theoretical weight: 7.38 KDa
Upstream strand DNA in PDB entry 7rpo, assembly 1, front view.
Upstream strand DNA in PDB entry 7rpo, assembly 1, side view.
Upstream strand DNA in PDB entry 7rpo, assembly 1, top view.
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DNA chain Y
Name: Downstream strand DNA
Representative chains: Y
Length: 23 nucleotides
Theoretical weight: 7.13 KDa
Downstream strand DNA in PDB entry 7rpo, assembly 1, front view.
Downstream strand DNA in PDB entry 7rpo, assembly 1, side view.
Downstream strand DNA in PDB entry 7rpo, assembly 1, top view.
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DNA chain Z
Name: Template strand DNA
Representative chains: Z
Length: 47 nucleotides
Theoretical weight: 14.4 KDa
Template strand DNA in PDB entry 7rpo, assembly 1, front view.
Template strand DNA in PDB entry 7rpo, assembly 1, side view.
Template strand DNA in PDB entry 7rpo, assembly 1, top view.
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