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: 6.00 Å

wwPDB Validation   3D Report Full Report


This is version 1.4 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 Biol 5: 441-446

  • DOI: https://doi.org/10.1038/nsb0698-441
  • Primary Citation of Related Structures:  
    1BDX

  • 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 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HOLLIDAY JUNCTION DNA HELICASE RUVAE [auth A],
F [auth B],
G [auth C],
H [auth D]
203Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for P0A809 (Escherichia coli (strain K12))
Explore P0A809 
Go to UniProtKB:  P0A809
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A809
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')A [auth J],
B [auth K],
C [auth L],
D [auth M]
16N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148α = 90
b = 148β = 123
c = 105.6γ = 90
Software Package:
Software NamePurpose
CCP4model building
MLPHAREphasing
Omodel building
DENZOdata reduction
CCP4data scaling
ROTAVATAdata scaling
CCP4phasing
TFFCphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-24
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Refinement description