1CLQ

CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX AT 2.7 A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.

Shamoo, Y., Steitz, T.A.

(1999) Cell 99: 155-166

  • DOI: 10.1016/s0092-8674(00)81647-5
  • Primary Citation of Related Structures:  
    1B77, 1B8H, 1CLQ

  • PubMed Abstract: 

    • We have solved the crystal structures of the bacteriophage RB69 sliding clamp, its complex with a peptide essential for DNA polymerase interactions, and the DNA polymerase complexed with primer-template DNA. The editing complex structure shows a partiall ...

    We have solved the crystal structures of the bacteriophage RB69 sliding clamp, its complex with a peptide essential for DNA polymerase interactions, and the DNA polymerase complexed with primer-template DNA. The editing complex structure shows a partially melted duplex DNA exiting from the exonuclease domain at an unexpected angle and significant changes in the protein structure. The clamp complex shows the C-terminal 11 residues of polymerase bound in a hydrophobic pocket, and it allows docking of the editing and clamp structures together. The peptide binds to the sliding clamp at a position identical to that of a replication inhibitor peptide bound to PCNA, suggesting that the replication inhibitor protein p21CIP1 functions by competing with eukaryotic polymerases for the same binding pocket on the clamp.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8814, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA POLYMERASE) A903Escherichia phage RB69Mutation(s): 0 
Gene Names: GENE 43, 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*GP*GP*AP*AP*CP*TP*AP*CP*T)-3')E11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*TP*AP*GP*TP*TP*CP*CP*GP*CP*G)-3')D12N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.284 
      • R-Value Work: 0.230 
      • R-Value Observed: 0.230 
      • Space Group: H 3
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 209.74α = 90
      b = 209.74β = 90
      c = 114.25γ = 120
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1999-10-28
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance