› 4esv

X-ray diffraction
3.2Å resolution

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

Released:
DOI: 10.2210/pdb4esv/pdb
PDB entry 4esv coloured by chain, front view.
PDB entry 4esv coloured by chain, side view.
PDB entry 4esv coloured by chain, top view.
Source organisms:
Primary publication:
The hexameric helicase DnaB adopts a nonplanar conformation during translocation.
Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA
Cell 151 267-77 (2012)
PMID: 23022319

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218962 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Replicative DNA helicase Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 454 amino acids
Theoretical weight: 50.7 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X4C9 (Residues: 1-454; Coverage: 100%)
Gene name: dnaB
Sequence domains:
Structure domains:
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' Chain: V
Molecule details ›
Chain: V
Length: 14 nucleotides
Theoretical weight: 4.21 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' Chain: W
Molecule details ›
Chain: W
Length: 13 nucleotides
Theoretical weight: 3.91 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MES 4 x MES
Ligand CA 14 x CA
Ligand GDP 10 x GDP
Ligand ALF 10 x ALF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C, NSLS BEAMLINE X25, NSLS BEAMLINE X29A
Spacegroup: P2221
Unit cell:
a: 149.124Å b: 180.321Å c: 279.128Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.245 0.242 0.289
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

37 review citations

Regulated protein turnover: snapshots of the proteasome in action.
Bhattacharyya et al. (2014)
36 more

31 mentions without citation

Replicating animal mitochondrial DNA.
McKinney et al. (2013)
30 more