3U61

Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

How a DNA polymerase clamp loader opens a sliding clamp.

Kelch, B.A.Makino, D.L.O'Donnell, M.Kuriyan, J.

(2011) Science 334: 1675-1680

  • DOI: 10.1126/science.1211884
  • Primary Citation of Related Structures:  
    3U60, 3U61, 3U5Z

  • PubMed Abstract: 
  • Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA ...

    Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.


    Organizational Affiliation

    Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase accessory protein 44 BCDE324Escherichia virus T4Mutation(s): 0 
Gene Names: 44gp44
Find proteins for P04526 (Enterobacteria phage T4)
Explore P04526 
Go to UniProtKB:  P04526
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase accessory protein 62 A199Escherichia virus T4Mutation(s): 0 
Gene Names: 62gp62
Find proteins for P04527 (Enterobacteria phage T4)
Explore P04527 
Go to UniProtKB:  P04527
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase processivity component FGH228Escherichia virus T4Mutation(s): 0 
Gene Names: 45gp45
Find proteins for P04525 (Enterobacteria phage T4)
Explore P04525 
Go to UniProtKB:  P04525
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    Template DNA strandI20N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 5
      MoleculeChainsLengthOrganismImage
      Primer DNA strandJ10N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      08T
      Query on 08T

      Download Ideal Coordinates CCD File 
      C, D
      [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
      C10 H14 Be F3 N5 O10 P2
      WOGYHYSOODLXII-KWIZKVQNSA-J
       Ligand Interaction
      ADP
      Query on ADP

      Download Ideal Coordinates CCD File 
      B
      ADENOSINE-5'-DIPHOSPHATE
      C10 H15 N5 O10 P2
      XTWYTFMLZFPYCI-KQYNXXCUSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      B, C, D
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      MSE
      Query on MSE
      F,G,HL-PEPTIDE LINKINGC5 H11 N O2 SeMET
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Free: 0.305 
      • R-Value Work: 0.239 
      • R-Value Observed: 0.244 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 82.303α = 90
      b = 137.272β = 90
      c = 222.779γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-01-04
        Type: Initial release