Biological Assembly 1  

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 108.04 kDa 
• Atom Count: 824 
• Modelled Residue Count: 824 
• Deposited Residue Count: 876 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1BDX

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

• PDB DOI: 10.2210/pdb1BDX/pdb
• NDB: PD0098

• Classification: TRANSFERASE/DNA
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-05-11 Released: 1999-11-24 
• Deposition Author(s): Hargreaves, D., Rice, D.W., Sedelnikova, S.E., Artymiuk, P.J., Lloyd, R.G., Rafferty, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.00 Å

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

• PubMed: 9628481 
• DOI: 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HOLLIDAY JUNCTION DNA HELICASE RUVA	E [auth A], F [auth B], G [auth C], H [auth D]	203	Escherichia coli BL21(DE3)	Mutation(s): 0  EC: 3.6.4.12
UniProt
Find proteins for P0A809 (Escherichia coli (strain K12)) Explore P0A809  Go to UniProtKB:  P0A809

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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]	16	N/A

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 = 148	α = 90
b = 148	β = 123
c = 105.6	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
MLPHARE	phasing
O	model building
DENZO	data reduction
CCP4	data scaling
ROTAVATA	data scaling
CCP4	phasing
TFFC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-24 
Deposition Author(s): Hargreaves, D., Rice, D.W., Sedelnikova, S.E., Artymiuk, P.J., Lloyd, R.G., Rafferty, J.B.

Revision History  

• 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