› 3gli

X-ray diffraction
3.5Å resolution

Crystal Structure of the E. coli clamp loader bound to Primer-Template DNA and Psi Peptide

Released:
DOI: 10.2210/pdb3gli/pdb
PDB entry 3gli coloured by chain, front view.
PDB entry 3gli coloured by chain, side view.
PDB entry 3gli coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J
Cell 137 659-71 (2009)
PMID: 19450514

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116310 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
DNA polymerase III subunit delta Chains: A, F
Molecule details ›
Chains: A, F
Length: 343 amino acids
Theoretical weight: 38.75 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P28630 (Residues: 1-343; Coverage: 100%)
Gene names: JW0635, b0640, holA
Sequence domains:
Structure domains:
DNA polymerase III subunit tau Chains: B, C, D, G, H, I
Molecule details ›
Chains: B, C, D, G, H, I
Length: 395 amino acids
Theoretical weight: 43.96 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P06710 (Residues: 1-373; Coverage: 58%)
Gene names: JW0459, b0470, dnaX, dnaZ, dnaZX
Sequence domains:
Structure domains:
DNA polymerase III subunit delta' Chains: E, J
Molecule details ›
Chains: E, J
Length: 334 amino acids
Theoretical weight: 36.98 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P28631 (Residues: 1-334; Coverage: 100%)
Gene names: JW1085, b1099, holB
Sequence domains:
Structure domains:
DNA polymerase III subunit psi Chains: O, P
Molecule details ›
Chains: O, P
Length: 27 amino acids
Theoretical weight: 3.19 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
UniProt:
  • Canonical: P28632 (Residues: 2-28; Coverage: 20%)
Gene names: JW4334, b4372, holD
DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3') Chains: K, M
Molecule details ›
Chains: K, M
Length: 15 nucleotides
Theoretical weight: 4.59 KDa
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3') Chains: L, N
Molecule details ›
Chains: L, N
Length: 10 nucleotides
Theoretical weight: 3.02 KDa

Ligands and Environments

4 bound ligands:
Ligand ADP 6 x ADP
Ligand BEF 6 x BEF
Ligand MG 6 x MG
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 98.69Å b: 217.18Å c: 275.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

17 review citations

DNA replicases from a bacterial perspective.
McHenry CS. (2011)
16 more

6 mentions without citation

Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target.
Robinson et al. (2012)
5 more