Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37968.49 
• Atom Count: 2417 
• Residue Count: 334 
• Unique protein chains: 1

1J7K

THERMOTOGA MARITIMA RUVB P216G MUTANT

• DOI: 10.2210/pdb1J7K/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2001-05-16 Released: 2001-08-08 
• Deposition Author(s): Putnam, C.D., Clancy, S.B., Tsuruta, H., Wetmur, J.G., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.238 
• R-Value Work: 0.212 

Literature

Structure and mechanism of the RuvB Holliday junction branch migration motor.

Putnam, C.D., Clancy, S.B., Tsuruta, H., Gonzalez, S., Wetmur, J.G., Tainer, J.A.

(2001) J.Mol.Biol. 311: 297-310

• PubMed: 11478862 
• DOI: 10.1006/jmbi.2001.4852
• Primary Citation of Related Structures:  
  1IN8, 1IN7, 1IN6, 1IN5, 1IN4


• PubMed Abstract: 
  

The RuvB hexamer is the chemomechanical motor of the RuvAB complex that migrates Holliday junction branch-points in DNA recombination and the rescue of stalled DNA replication forks. The 1.6 A crystal structure of Thermotoga maritima RuvB together with five mutant structures reveal that RuvB is an ATPase-associated with diverse cellular activities (AAA+-class ATPase) with a winged-helix DNA-binding domain. The RuvB-ADP complex structure and mutagenesis suggest how AAA+-class ATPases couple nucleotide binding and hydrolysis to interdomain conformational changes and asymmetry within the RuvB hexamer implied by the crystallographic packing and small-angle X-ray scattering in solution. ATP-driven domain motion is positioned to move double-stranded DNA through the hexamer and drive conformational changes between subunits by altering the complementary hydrophilic protein- protein interfaces. Structural and biochemical analysis of five motifs in the protein suggest that ATP binding is a strained conformation recognized both by sensors and the Walker motifs and that intersubunit activation occurs by an arginine finger motif reminiscent of the GTPase-activating proteins. Taken together, these results provide insights into how RuvB functions as a motor for branch migration of Holliday junctions.

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Organizational Affiliation: 

Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, MB 4, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HOLLIDAY JUNCTION DNA HELICASE RUVB	A	334	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)	Mutation(s): 1  Gene Names: ruvB EC: 3.6.4.12
Find proteins for Q56313 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)) Go to UniProtKB:  Q56313

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
HEZ	A	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO	A	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.238 
• R-Value Work: 0.212 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 86.217	α = 90.00
b = 86.217	β = 90.00
c = 82.142	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-16 
• Released Date: 2001-08-08 
• Deposition Author(s): Putnam, C.D., Clancy, S.B., Tsuruta, H., Wetmur, J.G., Tainer, J.A.

Revision History 

• Version 1.0: 2001-08-08
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance