3AAF

Structure of WRN RQC domain bound to double-stranded DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN

Kitano, K., Kim, S.Y., Hakoshima, T.

(2010) Structure 18: 177-187

  • DOI: 10.1016/j.str.2009.12.011
  • Primary Citation of Related Structures:  
    3AAF

  • PubMed Abstract: 

    • The RecQ family of DNA helicases including WRN (Werner syndrome protein) and BLM (Bloom syndrome protein) protects the genome against deleterious changes. Here we report the cocrystal structure of the RecQ C-terminal (RQC) domain of human WRN bound to a DNA duplex ...

    The RecQ family of DNA helicases including WRN (Werner syndrome protein) and BLM (Bloom syndrome protein) protects the genome against deleterious changes. Here we report the cocrystal structure of the RecQ C-terminal (RQC) domain of human WRN bound to a DNA duplex. In the complex, the RQC domain specifically interacted with a blunt end of the duplex and, surprisingly, unpaired a Watson-Crick base pair in the absence of an ATPase domain. The beta wing, an extended hairpin motif that is characteristic of winged-helix motifs, was used as a "separating knife" to wedge between the first and second base pairs, whereas the recognition helix, a principal component of helix-turn-helix motifs that are usually embedded within DNA grooves, was unprecedentedly excluded from the interaction. Our results demonstrate a function of the winged-helix motif central to the helicase reaction, establishing the first structural paradigm concerning the DNA structure-specific activities of the RecQ helicases.

    Organizational Affiliation: 

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. kkitano@is.naist.jp



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Werner syndrome ATP-dependent helicaseA, B134Homo sapiensMutation(s): 0 
Gene Names: WRN, RECQ3, RECQL2
EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt), 3.1 (UniProt)
Find proteins for Q14191 (Homo sapiens)
Explore Q14191 
Go to UniProtKB:  Q14191
NIH Common Fund Data Resources
PHAROS:  Q14191
GTEx:  ENSG00000165392
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3')C, D14N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ACT
    Query on ACT
    Download Ideal Coordinates CCD File 
    		 E [auth A], F [auth B]ACETATE ION
    C2 H3 O2
    QTBSBXVTEAMEQO-UHFFFAOYSA-M    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Free: 0.244 
    • R-Value Work: 0.212 
    • R-Value Observed: 0.213 
    • Space Group: P 43 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 84.077α = 90
    b = 84.077β = 90
    c = 145.291γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SHARPphasing
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2010-02-16
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Advisory, Refinement description, Version format compliance