5Y3C

Crystal structure of zebrafish Ccd1 DIX domain

  • Classification: SIGNALING PROTEIN
  • Organism(s): Danio rerio
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-07-28 Released: 2017-09-06 
  • Deposition Author(s): Terawaki, S., Shibata, N., Higuchi, Y.
  • Funding Organization(s): MEXT, JSPS, Hyogo Science and Technology Association, Sasakawa Scienti c Research Grant from the Japan Science Society, Sumitomo Foundation, Leave a Nest Grants Caliper Life Science Award, Uehara Memorial Foundation, Takeda Medical Science, Inamori Foundation, JAXA, Grant-in-Aid from the Global COE program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for Ccd1 auto-inhibition in the Wnt pathway through homomerization of the DIX domain.

Terawaki, S.I.Fujita, S.Katsutani, T.Shiomi, K.Keino-Masu, K.Masu, M.Wakamatsu, K.Shibata, N.Higuchi, Y.

(2017) Sci Rep 7: 7739-7739

  • DOI: https://doi.org/10.1038/s41598-017-08019-5
  • Primary Citation of Related Structures:  
    5Y3B, 5Y3C

  • PubMed Abstract: 

    Wnt signaling plays an important role in governing cell fate decisions. Coiled-coil-DIX1 (Ccd1), Dishevelled (Dvl), and Axin are signaling proteins that regulate the canonical pathway by controlling the stability of a key signal transducer β-catenin. These proteins contain the DIX domain with a ubiquitin-like fold, which mediates their interaction in the β-catenin destruction complex through dynamic head-to-tail polymerization. Despite high sequence similarities, mammalian Ccd1 shows weaker stimulation of β-catenin transcriptional activity compared with zebrafish (z) Ccd1 in cultured cells. Here, we show that the mouse (m) Ccd1 DIX domain displays weaker ability for homopolymerization than that of zCcd1. Furthermore, X-ray crystallographic analysis of mCcd1 and zCcd1 DIX domains revealed that mCcd1 was assembled into a double-helical filament by the insertion of the β1-β2 loop into the head-to-tail interface, whereas zCcd1 formed a typical single-helical polymer similar to Dvl1 and Axin. The mutation in the contact interface of mCcd1 double-helical polymer changed the hydrodynamic properties of mCcd1 so that it acquired the ability to induce Wnt-specific transcriptional activity similar to zCcd1. These findings suggest a novel regulatory mechanism by which mCcd1 modulates Wnt signaling through auto-inhibition of dynamic head-to-tail homopolymerization.


  • Organizational Affiliation

    Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan. terawaki@gunma-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dixin-A85Danio rerioMutation(s): 0 
Gene Names: dixdc1accd1dixdc1
UniProt
Find proteins for Q804T6 (Danio rerio)
Explore Q804T6 
Go to UniProtKB:  Q804T6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ804T6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.724α = 90
b = 46.724β = 90
c = 79.361γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan22121519
MEXTJapan23121527
MEXTJapan25121705
MEXTJapan23121526
MEXTJapan25121731
JSPSJapan22370061
JSPSJapan22770112
JSPSJapan25840017
Hyogo Science and Technology AssociationJapan--
Sasakawa Scienti c Research Grant from the Japan Science SocietyJapan--
Sumitomo Foundation--
Leave a Nest Grants Caliper Life Science AwardJapan--
Uehara Memorial FoundationJapan--
Takeda Medical ScienceJapan--
Inamori FoundationJapan--
JAXAJapan--
Grant-in-Aid from the Global COE programJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description