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 

wwPDB Validation   3D Report Full Report


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 requi ...

    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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(by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
HOLLIDAY JUNCTION DNA HELICASE RUVA A203Escherichia coliMutation(s): 0 
EC: 3.6.4.12
Find proteins for P0A809 (Escherichia coli (strain K12))
Explore P0A809 
Go to UniProtKB:  P0A809
Protein Feature View
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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')B13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')C12N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')D13N/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')E12N/A
          • Find similar nucleic acids by:  Sequence   |   Structure
            • Entity ID: 5
            MoleculeChainsLengthOrganismImage
            DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')F13N/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')G12N/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')H13N/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')I12N/A
                  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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                  View more in-depth experimental data

                  Entry History 

                  Deposition Data

                  Revision History 

                  • 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