1C7Y

E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 

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.USA 97: 8257-8262

  • DOI: 10.1073/pnas.140212997

  • 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 r ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
HOLLIDAY JUNCTION DNA HELICASE RUVA
A
203Escherichia coli (strain K12)Gene Names: ruvA
EC: 3.6.4.12
Find proteins for P0A809 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A809
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')B13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')C12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')D13N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')E12N/A
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')F13N/A
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')G12N/A
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')H13N/A
Entity ID: 8
MoleculeChainsLengthOrganism
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: 3.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 158.650α = 90.00
b = 158.650β = 90.00
c = 158.650γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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