1BDX

E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.

Hargreaves, D.Rice, D.W.Sedelnikova, S.E.Artymiuk, P.J.Lloyd, R.G.Rafferty, J.B.

(1998) Nat.Struct.Mol.Biol. 5: 441-446


  • PubMed Abstract: 
  • Here we present the crystal structure of the Escherichia coli protein RuvA bound to a key DNA intermediate in recombination, the Holliday junction. The structure, solved by isomorphous replacement and density modification at 6 A resolution, reveals t ...

    Here we present the crystal structure of the Escherichia coli protein RuvA bound to a key DNA intermediate in recombination, the Holliday junction. The structure, solved by isomorphous replacement and density modification at 6 A resolution, reveals the molecular architecture at the heart of the branch migration and resolution reactions required to process Holliday intermediates into recombinant DNA molecules. It also reveals directly for the first time the structure of the Holliday junction. A single RuvA tetramer is bound to one face of a junction whose four DNA duplex arms are arranged in an open and essentially four-fold symmetric conformation. Protein-DNA contacts are mediated by two copies of a helix-hairpin-helix motif per RuvA subunit that contact the phosphate backbone in a very similar manner. The open structure of the junction stabilized by RuvA binding exposes a DNA surface that could be bound by the RuvC endonuclease to promote resolution.


    Related Citations: 
    • Crystal Structure of DNA Recombination Protein Ruva and a Model for its Binding to the Holliday Junction
      Rafferty, J.B.,Sedelnikova, S.E.,Hargreaves, D.,Artymiuk, P.J.,Baker, P.J.,Sharples, G.J.,Mahdi, A.A.,Lloyd, R.G.,Rice, D.W.
      (1996) Science 274: 415


    Organizational Affiliation

    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HOLLIDAY JUNCTION DNA HELICASE RUVA
A, B, C, D
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*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')J,K,L,M16N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.000α = 90.00
b = 148.000β = 123.00
c = 105.600γ = 90.00
Software Package:
Software NamePurpose
CCP4model building
MLPHAREphasing
TFFCphasing
CCP4phasing
CCP4data scaling
ROTAVATAdata scaling
Omodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-24
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-22
    Type: Refinement description