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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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 interac ...

    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.,Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Segment polarity protein dishevelled homolog DVL-2
A
82Homo sapiensMutation(s): 2 
Gene Names: DVL2
Find proteins for O14641 (Homo sapiens)
Go to Gene View: DVL2
Go to UniProtKB:  O14641
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 44.470α = 90.00
b = 44.470β = 90.00
c = 87.650γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan23121526
Japan25121731

Revision History 

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