1IXS

Structure of RuvB complexed with RuvA domain III

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 

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This is version 1.3 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

  • DOI: https://doi.org/10.1016/s1097-2765(02)00641-x
  • Primary Citation of Related Structures:  
    1IXR, 1IXS

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Holliday junction DNA helicase ruvA62Thermus thermophilusMutation(s): 0 
Gene Names: ruva
UniProt
Find proteins for Q9F1Q3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q9F1Q3 
Go to UniProtKB:  Q9F1Q3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1Q3
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB318Thermus thermophilusMutation(s): 0 
Gene Names: ruvb
EC: 3.6.1.3
UniProt
Find proteins for Q5SL87 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SL87 
Go to UniProtKB:  Q5SL87
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SL87
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
C [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.06α = 90
b = 102.06β = 90
c = 137.75γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description