6IW3

High resolution structure of Dvl2-DIX Y27W/C80S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


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Literature

High-resolution structure of a Y27W mutant of the Dishevelled2 DIX domain.

Yamanishi, K.Sin, Y.Terawaki, S.I.Higuchi, Y.Shibata, N.

(2019) Acta Crystallogr F Struct Biol Commun 75: 116-122

  • DOI: 10.1107/S2053230X18018290
  • Primary Citation of Related Structures:  
    6IW3

  • PubMed Abstract: 
  • Dishevelled (Dvl) is a positive regulator of the canonical Wnt pathway that downregulates the phosphorylation of β-catenin and its subsequent degradation. Dvl contains an N-terminal DIX domain, which is involved in its homooligomerization and interactions with regulators of the Wnt pathway ...

    Dishevelled (Dvl) is a positive regulator of the canonical Wnt pathway that downregulates the phosphorylation of β-catenin and its subsequent degradation. Dvl contains an N-terminal DIX domain, which is involved in its homooligomerization and interactions with regulators of the Wnt pathway. The crystal structure of a Y27W mutant of the Dishevelled2 DIX domain (DIX-Y27W) has been determined at 1.64 Å resolution. DIX-Y27W has a compact ubiquitin-like fold and self-associates with neighbouring molecules through β-bridges, resulting in a head-to-tail helical molecular arrangement similar to previously reported structures of DIX domains. Glu23 of DIX-Y27W forms a hydrogen bond to the side chain of Trp27, corresponding to the Glu762...Trp766 hydrogen bond of the rat Axin DIX domain, whereas Glu23 in the Y27D mutant of the Dishevelled2 DIX domain forms a salt bridge to Lys68 of the adjacent molecule. The high-resolution DIX-Y27W structure provides details of the head-to-tail interaction, including solvent molecules, and also the plausibly wild-type-like structure of the self-association surface compared with previously published Dvl DIX-domain mutants.


    Organizational Affiliation

    Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako-gun, Hyogo 678-1297, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Segment polarity protein dishevelled homolog DVL-2A82Homo sapiensMutation(s): 2 
Gene Names: DVL2
UniProt & NIH Common Fund Data Resources
Find proteins for O14641 (Homo sapiens)
Explore O14641 
Go to UniProtKB:  O14641
PHAROS:  O14641
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14641
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.47α = 90
b = 44.47β = 90
c = 87.65γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan23121526
Japan25121731

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release