4P2J | pdb_00004p2j

Crystal structure of the mouse SNX19 PX domain with bound sulphate ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.263 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4P2J

This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Different Phosphoinositide Specificities of the PX Domains of Sorting Nexins Regulating G-protein Signaling.

Mas, C.Norwood, S.J.Bugarcic, A.Kinna, G.Leneva, N.Kovtun, O.Ghai, R.Ona Yanez, L.E.Davis, J.L.Teasdale, R.D.Collins, B.M.

(2014) J Biological Chem 289: 28554-28568

  • DOI: https://doi.org/10.1074/jbc.M114.595959
  • Primary Citation Related Structures: 
    4P2I, 4P2J, 4PQO, 4PQP

  • PubMed Abstract: 

    Sorting nexins (SNXs) or phox homology (PX) domain containing proteins are central regulators of cell trafficking and signaling. A subfamily of PX domain proteins possesses two unique PX-associated domains, as well as a regulator of G protein-coupled receptor signaling (RGS) domain that attenuates Gαs-coupled G protein-coupled receptor signaling. Here we delineate the structural organization of these RGS-PX proteins, revealing a protein family with a modular architecture that is conserved in all eukaryotes. The one exception to this is mammalian SNX19, which lacks the typical RGS structure but preserves all other domains. The PX domain is a sensor of membrane phosphoinositide lipids and we find that specific sequence alterations in the PX domains of the mammalian RGS-PX proteins, SNX13, SNX14, SNX19, and SNX25, confer differential phosphoinositide binding preferences. Although SNX13 and SNX19 PX domains bind the early endosomal lipid phosphatidylinositol 3-phosphate, SNX14 shows no membrane binding at all. Crystal structures of the SNX19 and SNX14 PX domains reveal key differences, with alterations in SNX14 leading to closure of the binding pocket to prevent phosphoinositide association. Our findings suggest a role for alternative membrane interactions in spatial control of RGS-PX proteins in cell signaling and trafficking.


  • Organizational Affiliation
    • From the Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia.

Macromolecule Content 

  • Total Structure Weight: 31.51 kDa 
  • Atom Count: 1,976 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 274 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MKIAA0254 protein
A, B
137Mus musculusMutation(s): 0 
Gene Names: Snx19mKIAA0254
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4T1 (Mus musculus)
Explore Q6P4T1 
Go to UniProtKB:  Q6P4T1
IMPC:  MGI:1921581
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P4T1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.263 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.172α = 90
b = 32.987β = 107.25
c = 82.509γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy