8HQL | pdb_00008hql

Crystal structure of mouse SNX25 PX domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Redox-modulated SNX25 as a novel regulator of GPCR-G protein signaling from endosomes.

Zhang, Y.Yu, Z.Sun, M.Du, R.Gao, H.Dai, Q.Dong, Y.Liu, C.Yin, M.Xu, T.Zhang, X.Liu, J.Xu, J.

(2024) Redox Biol 75: 103253-103253

  • DOI: https://doi.org/10.1016/j.redox.2024.103253
  • Primary Citation of Related Structures:  
    8HQL

  • PubMed Abstract: 

    GPCR-G protein signaling from endosomes plays a crucial role in various physiological and pathological processes. However, the mechanism by which endosomal G protein signaling is terminated remains largely unknown. In this study, we aimed to investigate the regulatory mechanisms involved in terminating the signaling of Gα subunits from endosomes. Through structural analysis and cell-based assays, we have discovered that SNX25, a protein that targets endosomes via its PXA or PXC domain, interacts with regulator of G protein signaling (RGS) proteins (including RGS2, RGS4, RGS8, and RGS17) in a redox-regulated manner. The interaction between SNX25 and these RGS proteins enhances their GTPase-accelerating activity towards Gα i/q and their ability to bind GDP-bound (inactive form) Gα i/q . As a result, SNX25 recruits these RGS proteins to endosomes, leading to the termination of endosomal Gα i/q signaling. Furthermore, we have found that the SNX25/RGS complex also exerts a negative regulatory effect on Gα i/q signaling from the plasma membrane. This is achieved by recruiting Gα i/q to endosomes and preventing its activation on the plasma membrane. Our findings shed light on the previously unknown role of redox-modulated SNX25 in inhibiting Gα i/q signaling, thereby uncovering a novel mechanism for terminating Gα i/q signaling from endosomes. Importantly, this study expands our understanding of the regulation of GPCR-Gα i/q signaling beyond the plasma membrane.


  • 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-25
A, B, C, D, E
128Mus musculusMutation(s): 0 
Gene Names: Snx25
UniProt & NIH Common Fund Data Resources
Find proteins for Q3ZT31 (Mus musculus)
Explore Q3ZT31 
Go to UniProtKB:  Q3ZT31
IMPC:  MGI:2142610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3ZT31
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE (Subject of Investigation/LOI)
Query on 1PE

Download Ideal Coordinates CCD File 
EA [auth D]
F [auth A]
FA [auth D]
G [auth A]
GA [auth D]
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
LA [auth E],
MA [auth E],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
W [auth C]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
IA [auth D]
J [auth A]
K [auth A]
AA [auth C],
BA [auth C],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
NA [auth E],
OA [auth E],
PA [auth E],
X [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY (Subject of Investigation/LOI)
Query on ACY

Download Ideal Coordinates CCD File 
DA [auth C],
KA [auth D]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C],
JA [auth D],
O [auth A],
QA [auth E],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.68α = 90
b = 92.68β = 90
c = 449.521γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary