1JR3

Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III.

Jeruzalmi, D.O'Donnell, M.Kuriyan, J.

(2001) Cell 106: 429-441


  • PubMed Abstract: 
  • The gamma complex, an AAA+ ATPase, is the bacterial homolog of eukaryotic replication factor C (RFC) that loads the sliding clamp (beta, homologous to PCNA) onto DNA. The 2.7/3.0 A crystal structure of gamma complex reveals a pentameric arrangement o ...

    The gamma complex, an AAA+ ATPase, is the bacterial homolog of eukaryotic replication factor C (RFC) that loads the sliding clamp (beta, homologous to PCNA) onto DNA. The 2.7/3.0 A crystal structure of gamma complex reveals a pentameric arrangement of subunits, with stoichiometry delta':gamma(3):delta. The C-terminal domains of the subunits form a circular collar that supports an asymmetric arrangement of the N-terminal ATP binding domains of the gamma motor and the structurally related domains of the delta' stator and the delta wrench. The structure suggests a mechanism by which the gamma complex switches between a closed state, in which the beta-interacting element of delta is hidden by delta', and an open form similar to the crystal structure, in which delta is free to bind to beta.


    Organizational Affiliation

    Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit gamma
A, B, C
373Escherichia coli (strain K12)Gene Names: dnaX (dnaZ, dnaZX)
EC: 2.7.7.7
Find proteins for P06710 (Escherichia coli (strain K12))
Go to UniProtKB:  P06710
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III, delta subunit
D
343Escherichia coli (strain K12)Gene Names: holA
EC: 2.7.7.7
Find proteins for P28630 (Escherichia coli (strain K12))
Go to UniProtKB:  P28630
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III, delta' subunit
E
334Escherichia coli (strain K12)Gene Names: holB
EC: 2.7.7.7
Find proteins for P28631 (Escherichia coli (strain K12))
Go to UniProtKB:  P28631
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.268 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.698α = 90.00
b = 95.857β = 90.00
c = 285.410γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation