5WY2

Human Snx5 PX domain in complex with Chlamydia IncE C terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional insights into sorting nexin 5/6 interaction with bacterial effector IncE.

Sun, Q.Yong, X.Sun, X.Yang, F.Dai, Z.Gong, Y.Zhou, L.Zhang, X.Niu, D.Dai, L.Liu, J.J.Jia, D.

(2017) Signal Transduct Target Ther 2: 17030-17030

  • DOI: https://doi.org/10.1038/sigtrans.2017.30
  • Primary Citation of Related Structures:  
    5WY2

  • PubMed Abstract: 

    The endosomal trafficking pathways are essential for many cellular activities. They are also important targets by many intracellular pathogens. Key regulators of the endosomal trafficking include the retromer complex and sorting nexins (SNXs). Chlamydia trachomatis effector protein IncE directly targets the retromer components SNX5 and SNX6 and suppresses retromer-mediated transport, but the exact mechanism has remained unclear. We present the crystal structure of the PX domain of SNX5 in complex with IncE, showing that IncE binds to a highly conserved hydrophobic groove of SNX5. The unique helical hairpin of SNX5/6 is essential for binding, explaining the specificity of SNX5/6 for IncE. The SNX5/6-IncE interaction is required for cellular localization of IncE and its inhibitory function. Mechanistically, IncE inhibits the association of CI-MPR cargo with retromer-containing endosomal subdomains. Our study provides new insights into the regulation of retromer-mediated transport and illustrates the intricate competition between host and pathogens in controlling cellular trafficking.


  • Organizational Affiliation

    Department of Pathology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-5
A, C
163Homo sapiensMutation(s): 0 
Gene Names: SNX5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5X3 (Homo sapiens)
Explore Q9Y5X3 
Go to UniProtKB:  Q9Y5X3
PHAROS:  Q9Y5X3
GTEx:  ENSG00000089006 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5X3
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IncE
B, D
21Chlamydia trachomatisMutation(s): 0 
UniProt
Find proteins for B7SCI5 (Chlamydia trachomatis)
Explore B7SCI5 
Go to UniProtKB:  B7SCI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7SCI5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.443α = 94.79
b = 43.711β = 99.81
c = 60.07γ = 100.97
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NSFCChina81502629

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description