Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52644.71 
• Atom Count: 3565 
• Residue Count: 303 
• Unique protein chains: 1
• Unique nucleic acid chains: 8

1C7Y

E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX

• DOI: 10.2210/pdb1C7Y/pdb
• NDB: PD0136

• Classification: RECOMBINATION/DNA
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2000-04-03 Released: 2000-07-21 
• Deposition Author(s): Ariyoshi, M., Nishino, T., Iwasaki, H., Shinagawa, H., Morikawa, K.

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Experimental Data Snapshot

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

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

• PubMed: 10890893 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
HOLLIDAY JUNCTION DNA HELICASE RUVA	A	203	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: ruvA EC: 3.6.4.12
Find proteins for P0A809 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A809

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')	B	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')	C	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')	D	13	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')	E	12	N/A

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')	F	13	N/A

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')	G	12	N/A

Entity ID: 7
Molecule	Chains	Length	Organism
DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')	H	13	N/A

Entity ID: 8
Molecule	Chains	Length	Organism
DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')	I	12	N/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 = 158.650	α = 90.00
b = 158.650	β = 90.00
c = 158.650	γ = 90.00

Software Package:

Software Name	Purpose
MLPHARE	phasing
SCALEPACK	data scaling
DENZO	data reduction
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-03 
• Released Date: 2000-07-21 
• Deposition Author(s): Ariyoshi, M., Nishino, T., Iwasaki, H., Shinagawa, H., Morikawa, K.

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