Crystal structure of the human SNX25 regulator of G-protein signalling (RGS) domain

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural Predictions of the SNX-RGS Proteins Suggest They Belong to a New Class of Lipid Transfer Proteins.

Paul, B.Weeratunga, S.Tillu, V.A.Hariri, H.Henne, W.M.Collins, B.M.

(2022) Front Cell Dev Biol 10: 826688-826688

  • DOI: https://doi.org/10.3389/fcell.2022.826688
  • Primary Citation of Related Structures:  
    7SR1, 7SR2

  • PubMed Abstract: 

    Recent advances in protein structure prediction using machine learning such as AlphaFold2 and RosettaFold presage a revolution in structural biology. Genome-wide predictions of protein structures are providing unprecedented insights into their architecture and intradomain interactions, and applications have already progressed towards assessing protein complex formation. Here we present detailed analyses of the sorting nexin proteins that contain regulator of G-protein signalling domains (SNX-RGS proteins), providing a key example of the ability of AlphaFold2 to reveal novel structures with previously unsuspected biological functions. These large proteins are conserved in most eukaryotes and are known to associate with lipid droplets (LDs) and sites of LD-membrane contacts, with key roles in regulating lipid metabolism. They possess five domains, including an N-terminal transmembrane domain that anchors them to the endoplasmic reticulum, an RGS domain, a lipid interacting phox homology (PX) domain and two additional domains named the PXA and PXC domains of unknown structure and function. Here we report the crystal structure of the RGS domain of sorting nexin 25 (SNX25) and show that the AlphaFold2 prediction closely matches the experimental structure. Analysing the full-length SNX-RGS proteins across multiple homologues and species we find that the distant PXA and PXC domains in fact fold into a single unique structure that notably features a large and conserved hydrophobic pocket. The nature of this pocket strongly suggests a role in lipid or fatty acid binding, and we propose that these molecules represent a new class of conserved lipid transfer proteins.

  • Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-25
A, B
124Homo sapiensMutation(s): 1 
Gene Names: SNX25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3E2 (Homo sapiens)
Explore Q9H3E2 
Go to UniProtKB:  Q9H3E2
GTEx:  ENSG00000109762 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3E2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.035α = 90
b = 75.864β = 109.27
c = 51.109γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP200102551
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1136021

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description