3U5Z

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    3U5Z, 3U60, 3U61

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase accessory protein 44A [auth B], B [auth C], C [auth D], D [auth E], K [auth L], L [auth M], M [auth N], N [auth O]324Escherichia virus T4Mutation(s): 0 
Gene Names: 44gp44
UniProt
Find proteins for P04526 (Enterobacteria phage T4)
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Go to UniProtKB:  P04526
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase accessory protein 62E [auth A], O [auth K]199Escherichia virus T4Mutation(s): 0 
Gene Names: 62gp62
UniProt
Find proteins for P04527 (Enterobacteria phage T4)
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Go to UniProtKB:  P04527
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase processivity componentH [auth F], F [auth G], G [auth H], R [auth P], P [auth Q], Q [auth R]228Escherichia virus T4Mutation(s): 0 
Gene Names: 45gp45
UniProt
Find proteins for P04525 (Enterobacteria phage T4)
Explore P04525 
Go to UniProtKB:  P04525
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
Template DNA strandI, S30N/A
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  • Reference Sequence
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  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    Primer DNA strandJ, T20N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    08T (Subject of Investigation/LOI)
    Query on 08T

    Download Ideal Coordinates CCD File 
    CA [auth L], EA [auth M], GA [auth N], U [auth B], W [auth C], Y [auth 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 (Subject of Investigation/LOI)
    Query on ADP

    Download Ideal Coordinates CCD File 
    AA [auth E], IA [auth O]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    BA [auth E], DA [auth L], FA [auth M], HA [auth N], JA [auth O], V [auth B], X [auth C], Z [auth D]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MSE
    Query on MSE
    F [auth G], G [auth H], H [auth F], P [auth Q], Q [auth R], R [auth P]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.50 Å
    • R-Value Free: 0.279 
    • R-Value Work: 0.231 
    • R-Value Observed: 0.232 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 95.702α = 90
    b = 239.177β = 90
    c = 247.672γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    AutoSolphasing
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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