7WF6 | pdb_00007wf6

Crystal structure of SNX13 RGS domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.224 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7WF6

This is version 1.1 of the entry. See complete history

Literature

Structural Studies Reveal Unique Non-canonical Regulators of G Protein Signaling Homology (RH) Domains in Sorting Nexins.

Zhang, Y.Chen, R.Dong, Y.Zhu, J.Su, K.Liu, J.Xu, J.

(2022) J Mol Biology 434: 167823-167823

  • DOI: https://doi.org/10.1016/j.jmb.2022.167823
  • Primary Citation Related Structures: 
    7WF6, 7WF8, 7WF9

  • PubMed Abstract: 

    As a subgroup of sorting nexins (SNXs) that contain regulator of G protein signaling homology (RH) domain, SNX-RH proteins, including SNX13, SNX14 and SNX25, were proposed to play bifunctional roles in protein sorting and GPCR signaling regulation. However, mechanistic details of SNX-RH proteins functioning via RH domain remain to be illustrated. Here, we delineate crystal structures of the RH domains of SNX13 and SNX25, revealing a homodimer of SNX13 RH domain mediated by unique extended α4 and α5 helices, and a thiol modulated homodimer of SNX25-RH triggered by a unique cysteine on α6 helix. Further studies showed that RH domains of SNX-RH do not possess binding capacity toward Gα subunits, owing to the lack of critical residues for interaction. Thus, this study identifies a group of novel non-canonical RH domains that can act as a dimerization module in sorting nexins, which provides structural basis for mechanism studies on SNX-RH protein functions.


  • Organizational Affiliation
    • State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Macromolecule Content 

  • Total Structure Weight: 18.04 kDa 
  • Atom Count: 1,203 
  • Modeled Residue Count: 145 
  • Deposited Residue Count: 152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sorting nexin-13152Homo sapiensMutation(s): 0 
Gene Names: SNX13KIAA0713
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5W8 (Homo sapiens)
Explore Q9Y5W8 
Go to UniProtKB:  Q9Y5W8
PHAROS:  Q9Y5W8
GTEx:  ENSG00000071189 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5W8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free:  0.224 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.328α = 90
b = 165.328β = 90
c = 165.328γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171213

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description