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Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode

Electron Microscopy
6.7Å resolution
PDB entry 5m1s coloured by chain, front view.
PDB entry 5m1s coloured by chain, side view.
PDB entry 5m1s coloured by chain, top view.
Source organism: Escherichia coli K-12
Assembly composition:
hetero heptamer (preferred)
Entry contents: 4 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA polymerase III core complex and Beta sliding clamp and DNA
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Multimeric state: hetero heptamer
Accessible surface area: 91736.35 Å2
Buried surface area: 16936.53 Å2
Dissociation area: 687.68 Å2
Dissociation energy (ΔGdiss): 2.44 kcal/mol
Dissociation entropy (TΔSdiss): 11.15 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-119003

Macromolecules

DNA polymerase III subunit alpha
Chain: A
Length: 927 amino acids
Theoretical weight: 103.55 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P10443 (Residues: 1-927; Coverage: 80%)
Gene names: JW0179, b0184, dnaE, polC
Pfam:
InterPro:
DNA polymerase III subunit alpha in PDB entry 5m1s, assembly 1, front view.
DNA polymerase III subunit alpha in PDB entry 5m1s, assembly 1, side view.
DNA polymerase III subunit alpha in PDB entry 5m1s, assembly 1, top view.
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Beta sliding clamp
Chains: B, C
Length: 366 amino acids
Theoretical weight: 40.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A988 (Residues: 1-366; Coverage: 100%)
Gene names: JW3678, b3701, dnaN
Pfam:
InterPro:
Beta sliding clamp in PDB entry 5m1s, assembly 1, front view.
Beta sliding clamp in PDB entry 5m1s, assembly 1, side view.
Beta sliding clamp in PDB entry 5m1s, assembly 1, top view.
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DNA polymerase III subunit epsilon
Chain: D
Length: 243 amino acids
Theoretical weight: 27.12 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P03007 (Residues: 1-243; Coverage: 100%)
Gene names: JW0205, b0215, dnaQ, mutD
Pfam: Exonuclease
InterPro:
DNA polymerase III subunit epsilon in PDB entry 5m1s, assembly 1, front view.
DNA polymerase III subunit epsilon in PDB entry 5m1s, assembly 1, side view.
DNA polymerase III subunit epsilon in PDB entry 5m1s, assembly 1, top view.
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DNA polymerase III subunit theta
Chain: F
Length: 56 amino acids
Theoretical weight: 6.5 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0ABS8 (Residues: 10-65; Coverage: 74%)
Gene names: JW1831, b1842, holE
Pfam: DNA polymerase III, theta subunit
InterPro:
DNA polymerase III subunit theta in PDB entry 5m1s, assembly 1, front view.
DNA polymerase III subunit theta in PDB entry 5m1s, assembly 1, side view.
DNA polymerase III subunit theta in PDB entry 5m1s, assembly 1, top view.
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DNA chain P
Name: DNA Primer Strand
Representative chains: P
Length: 17 nucleotides
Theoretical weight: 5.28 KDa
DNA Primer Strand in PDB entry 5m1s, assembly 1, front view.
DNA Primer Strand in PDB entry 5m1s, assembly 1, side view.
DNA Primer Strand in PDB entry 5m1s, assembly 1, top view.
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DNA chain T
Name: DNA Template Strand
Representative chains: T
Length: 22 nucleotides
Theoretical weight: 6.72 KDa
DNA Template Strand in PDB entry 5m1s, assembly 1, front view.
DNA Template Strand in PDB entry 5m1s, assembly 1, side view.
DNA Template Strand in PDB entry 5m1s, assembly 1, top view.
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