1C7Y

E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer.

Ariyoshi, M.Nishino, T.Iwasaki, H.Shinagawa, H.Morikawa, K.

(2000) Proc Natl Acad Sci U S A 97: 8257-8262

  • DOI: 10.1073/pnas.140212997
  • Primary Citation of Related Structures:  
    1C7Y

  • PubMed Abstract: 
  • In the major pathway of homologous DNA recombination in prokaryotic cells, the Holliday junction intermediate is processed through its association with RuvA, RuvB, and RuvC proteins. Specific binding of the RuvA tetramer to the Holliday junction is required for the RuvB motor protein to be loaded onto the junction DNA, and the RuvAB complex drives the ATP-dependent branch migration ...

    In the major pathway of homologous DNA recombination in prokaryotic cells, the Holliday junction intermediate is processed through its association with RuvA, RuvB, and RuvC proteins. Specific binding of the RuvA tetramer to the Holliday junction is required for the RuvB motor protein to be loaded onto the junction DNA, and the RuvAB complex drives the ATP-dependent branch migration. We solved the crystal structure of the Holliday junction bound to a single Escherichia coli RuvA tetramer at 3.1-A resolution. In this complex, one side of DNA is accessible for cleavage by RuvC resolvase at the junction center. The refined junction DNA structure revealed an open concave architecture with a four-fold symmetry. Each arm, with B-form DNA, in the Holliday junction is predominantly recognized in the minor groove through hydrogen bonds with two repeated helix-hairpin-helix motifs of each RuvA subunit. The local conformation near the crossover point, where two base pairs are disrupted, suggests a possible scheme for successive base pair rearrangements, which may account for smooth Holliday junction movement without segmental unwinding.


    Organizational Affiliation

    Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.



Macromolecules

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
HOLLIDAY JUNCTION DNA HELICASE RUVAI [auth A]203Escherichia coliMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for P0A809 (Escherichia coli (strain K12))
Explore P0A809 
Go to UniProtKB:  P0A809
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A809
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')A [auth B]13N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')B [auth C]12N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')C [auth D]13N/A
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')D [auth E]12N/A
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')E [auth F]13N/A
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')F [auth G]12N/A
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')G [auth H]13N/A
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')H [auth I]12N/A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.65α = 90
b = 158.65β = 90
c = 158.65γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-21
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance