› 8vam

Electron Microscopy
3.9Å resolution

Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation

Released:
DOI: 10.2210/pdb8vam/pdb
PDB entry 8vam coloured by chain, front view.
PDB entry 8vam coloured by chain, side view.
PDB entry 8vam coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA
J Biol Chem 107166 (2024)
PMID: 38490435
Related structures: EMD-43095

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-242273 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DNA polymerase III subunit delta Chain: A
Molecule details ›
Chain: A
Length: 333 amino acids
Theoretical weight: 37.69 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P28630 (Residues: 1-333; Coverage: 97%)
Gene names: JW0635, b0640, holA
Sequence domains:
DNA polymerase III subunit tau Chains: B, C, D
Molecule details ›
Chains: B, C, D
Length: 376 amino acids
Theoretical weight: 41.8 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06710 (Residues: 1-373; Coverage: 58%)
Gene names: JW0459, b0470, dnaX, dnaZ, dnaZX
Sequence domains:
DNA polymerase III subunit delta' Chain: E
Molecule details ›
Chain: E
Length: 337 amino acids
Theoretical weight: 37.27 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P28631 (Residues: 1-334; Coverage: 100%)
Gene names: JW1085, b1099, holB
Sequence domains:
Beta sliding clamp Chains: F, G
Molecule details ›
Chains: F, G
Length: 369 amino acids
Theoretical weight: 40.92 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A988 (Residues: 1-366; Coverage: 100%)
Gene names: JW3678, b3701, dnaN
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand ADP 3 x ADP
Ligand BEF 3 x BEF
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-43095
Expression system: Escherichia coli BL21(DE3)

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