1IXS

Structure of RuvB complexed with RuvA domain III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery

Yamada, K.Miyata, T.Tsuchiya, D.Oyama, T.Fujiwara, Y.Ohnishi, T.Iwasaki, H.Shinagawa, H.Ariyoshi, M.Mayanagi, K.Morikawa, K.

(2002) Mol.Cell 10: 671-681

  • Primary Citation of Related Structures:  1IXR

  • PubMed Abstract: 
  • We present the X-ray structure of the RuvA-RuvB complex, which plays a crucial role in ATP-dependent branch migration. Two RuvA tetramers form the symmetric and closed octameric shell, where four RuvA domain IIIs spring out in the two opposite direct ...

    We present the X-ray structure of the RuvA-RuvB complex, which plays a crucial role in ATP-dependent branch migration. Two RuvA tetramers form the symmetric and closed octameric shell, where four RuvA domain IIIs spring out in the two opposite directions to be individually caught by a single RuvB. The binding of domain III deforms the protruding beta hairpin in the N-terminal domain of RuvB and thereby appears to induce a functional and less symmetric RuvB hexameric ring. The model of the RuvA-RuvB junction DNA ternary complex, constructed by fitting the X-ray structure into the averaged electron microscopic images of the RuvA-RuvB junction, appears to be more compatible with the branch migration mode of a fixed RuvA-RuvB interaction than with a rotational interaction mode.


    Organizational Affiliation

    Biomolecular Engineering Research Institute, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Holliday junction DNA helicase ruvA
A
62Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: ruvA
EC: 3.6.4.12
Find proteins for Q9F1Q3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9F1Q3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RuvB
B
318Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: ruvB
EC: 3.6.4.12
Find proteins for Q5SL87 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SL87
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.060α = 90.00
b = 102.060β = 90.00
c = 137.750γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
AMoREphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance