5XDZ

Crystal structure of zebrafish SNX25 PX domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the PX domain of SNX25 reveals a novel phospholipid recognition model by dimerization in the PX domain

Su, K.Xu, T.Yu, Z.Zhu, J.Zhang, Y.Wu, M.Xiong, Y.Liu, J.Xu, J.

(2017) FEBS Lett 591: 2011-2018

  • DOI: https://doi.org/10.1002/1873-3468.12688
  • Primary Citation of Related Structures:  
    5XDZ

  • PubMed Abstract: 

    SNX25, a regulator of GPCR signaling-phox-homology (PX) domain containing sorting nexin (SNX) member, has been proposed to be involved in the lysosomal degradation of the transforming growth factor β receptor and the development of temporal lobe epilepsy. Targeting to the endosomal membranes by the specific binding of phosphorylated phosphatidylinositols (PIPs) through the PX domain is critical for the function of SNXs. However, the mechanism for SNX25-PX targeting to the endosomes remains unclear. Here, we demonstrate that the PX domain of zebrafish SNX25 (zSNX25-PX) is capable of binding to PI3P only in its dimeric form. We also present the crystal structure of zSNX25-PX. Combined with biochemical experiments, we further identify a potential PI3P-binding region and propose a novel PI-binding model based on dimerization in the PX domain of SNXs.


  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular trafficking proteinA [auth B]122Danio rerioMutation(s): 0 
Gene Names: snx25
UniProt
Find proteins for C6K2H9 (Danio rerio)
Explore C6K2H9 
Go to UniProtKB:  C6K2H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6K2H9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular trafficking proteinB [auth A]121Danio rerioMutation(s): 0 
Gene Names: snx25
UniProt
Find proteins for C6K2H9 (Danio rerio)
Explore C6K2H9 
Go to UniProtKB:  C6K2H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6K2H9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.15α = 90
b = 82.83β = 90
c = 36.5γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description