Nucleotide-free form of an Isolated E. coli Clamp Loader Gamma Subunit

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

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Nucleotide-Induced Conformational Changes in an Isolated Escherichia coli DNA Polymerase III Clamp Loader Subunit

Podobnik, M.Weitze, T.F.O'Donnell, M.Kuriyan, J.

(2003) Structure 11: 253-263

  • DOI: https://doi.org/10.1016/s0969-2126(03)00027-3
  • Primary Citation of Related Structures:  
    1NJF, 1NJG

  • PubMed Abstract: 

    Sliding clamps are loaded onto DNA by ATP-driven clamp loader complexes. The structure of the E. coli clamp loader in a nucleotide-free state has been determined previously. We now report crystal structures of a truncated form of the isolated gamma-ATPase subunit, gamma(1-243), of the E. coli clamp loader, in nucleotide-free and bound forms. The gamma subunit adopts a defined conformation when empty, in which the nucleotide binding site is blocked. The binding of either ATPgammaS or ADP, which are shown to bind with equal affinity to gamma(1-243), induces a change in the relative orientation of the two domains such that nucleotides can be accommodated. This change would break one of the gamma:gamma interfaces seen in the empty clamp loader complex, and may represent one step in the activation process.

  • Organizational Affiliation

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit gamma
A, B
250Escherichia coliMutation(s): 0 
Gene Names: dnaX
Find proteins for P06710 (Escherichia coli (strain K12))
Explore P06710 
Go to UniProtKB:  P06710
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06710
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.335α = 90
b = 85.471β = 93.15
c = 56.932γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description