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
  • Primary Citation of Related Structures:  
    3BEP

  • 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 into the protein-binding pocket of the clamp ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit betaC [auth A], D [auth B]366Escherichia coliMutation(s): 0 
Gene Names: dnaN
EC: 2.7.7.7
Find proteins for P0A988 (Escherichia coli (strain K12))
Explore P0A988 
Go to UniProtKB:  P0A988
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3')A [auth C]10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3')B [auth D]14N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      5CY
      Query on 5CY

      Download Ideal Coordinates CCD File 
      E [auth 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-y l}-3,3-dimethyl-3H-indolium
      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 = 113.284
      b = 70.08β = 92.073
      c = 73.872γ = 99.361
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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