3BEP

Structure of a sliding clamp on DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a sliding clamp on DNA

Georgescu, R.E.Kim, S.S.Yurieva, O.Kuriyan, J.Kong, X.-P.O'Donnell, M.

(2008) Cell 132: 43-54

  • DOI: 10.1016/j.cell.2007.11.045

  • PubMed Abstract: 
  • The structure of the E. coli beta clamp polymerase processivity factor has been solved in complex with primed DNA. Interestingly, the clamp directly binds the DNA duplex and also forms a crystal contact with the ssDNA template strand, which binds int ...

    The structure of the E. coli beta clamp polymerase processivity factor has been solved in complex with primed DNA. Interestingly, the clamp directly binds the DNA duplex and also forms a crystal contact with the ssDNA template strand, which binds into the protein-binding pocket of the clamp. We demonstrate that these clamp-DNA interactions function in clamp loading, perhaps by inducing the ring to close around DNA. Clamp binding to template ssDNA may also serve to hold the clamp at a primed site after loading or during switching of multiple factors on the clamp. Remarkably, the DNA is highly tilted as it passes through the beta ring. The pronounced 22 degrees angle of DNA through beta may enable DNA to switch between multiple factors bound to a single clamp simply by alternating from one protomer of the ring to the other.


    Organizational Affiliation

    Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, Box 228, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit beta
A, B
366Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaN
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3')C10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3')D14N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5CY
Query on 5CY

Download SDF File 
Download CCD File 
C
1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-yl}-3,3-dimethyl-3H-indolium
N,N'-(dipropyl)-tetramethylindodicarbocyanine
C31 H39 N2 O2
VFBDPICHYNKCQJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.210 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.203α = 113.28
b = 70.080β = 92.07
c = 73.872γ = 99.36
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Advisory, Refinement description