4P2I

Crystal structure of the mouse SNX19 PX domain

• PDB DOI:  https://doi.org/10.2210/pdb4P2I/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-04 Released: 2014-09-03 
• Deposition Author(s): Collins, B.M.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.247 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

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 Biol Chem 289: 28554-28568

• PubMed: 25148684 
• DOI: https://doi.org/10.1074/jbc.M114.595959
• Primary Citation of 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.

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Organizational Affiliation: 

From the Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.32 kDa 
• Atom Count: 2,205 
• Modelled Residue Count: 231 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MKIAA0254 protein	A, B	137	Mus musculus	Mutation(s): 0  Gene Names: Snx19, mKIAA0254, Kiaa0254
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4T1 (Mus musculus) Explore Q6P4T1  Go to UniProtKB:  Q6P4T1
IMPC:  MGI:1921581

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.247 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.84	α = 90
b = 32.938	β = 107.52
c = 81.966	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Collins, B.M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FT100100027
Australian Research Council (ARC)	Australia	DP0985029

Revision History  

• 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: 2018-01-17
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence