› 8vat

Electron Microscopy
3.2Å resolution

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

Released:
DOI: 10.2210/pdb8vat/pdb
PDB entry 8vat coloured by chain, front view.
PDB entry 8vat coloured by chain, side view.
PDB entry 8vat 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-43102

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 nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-242205 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (6 distinct):
DNA polymerase III subunit delta Chain: A
Molecule details ›
Chain: A
Length: 343 amino acids
Theoretical weight: 38.75 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P28630 (Residues: 1-343; Coverage: 100%)
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:
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*AP*GP*AP*CP*AP*CP*CP*AP*CP*TP*GP*C)-3') Chain: I
Molecule details ›
Chain: I
Length: 30 nucleotides
Theoretical weight: 9.07 KDa
RNA (5'-R(P*AP*GP*UP*GP*GP*UP*GP*UP*CP*UP*G)-3') Chain: H
Molecule details ›
Chain: H
Length: 11 nucleotides
Theoretical weight: 3.54 KDa

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: 3.2Å
Relevant EMDB volumes: EMD-43102
Expression system: Escherichia coli BL21(DE3)

Quick links