5TP1 | pdb_00005tp1

The structure of the C-terminus of virulence protein IncE from Chlamydia trachomatis bound to Mus musculus SNX5-PX domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.260 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5TP1

This is version 1.3 of the entry. See complete history

Literature

Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction.

Elwell, C.A.Czudnochowski, N.von Dollen, J.Johnson, J.R.Nakagawa, R.Mirrashidi, K.Krogan, N.J.Engel, J.N.Rosenberg, O.S.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.22709
  • Primary Citation Related Structures: 
    5TP1

  • PubMed Abstract: 

    Chlamydia trachomatis is an obligate intracellular pathogen that resides in a membrane-bound compartment, the inclusion. The bacteria secrete a unique class of proteins, Incs, which insert into the inclusion membrane and modulate the host-bacterium interface. We previously reported that IncE binds specifically to the Sorting Nexin 5 Phox domain (SNX5-PX) and disrupts retromer trafficking. Here, we present the crystal structure of the SNX5-PX:IncE complex, showing IncE bound to a unique and highly conserved hydrophobic groove on SNX5. Mutagenesis of the SNX5-PX:IncE binding surface disrupts a previously unsuspected interaction between SNX5 and the cation-independent mannose-6-phosphate receptor (CI-MPR). Addition of IncE peptide inhibits the interaction of CI-MPR with SNX5. Finally, C. trachomatis infection interferes with the SNX5:CI-MPR interaction, suggesting that IncE and CI-MPR are dependent on the same binding surface on SNX5. Our results provide new insights into retromer assembly and underscore the power of using pathogens to discover disease-related cell biology.


  • Organizational Affiliation
    • Department of Medicine, University of California, San Francisco, San Francisco, United States.

Macromolecule Content 

  • Total Structure Weight: 86.52 kDa 
  • Atom Count: 5,801 
  • Modeled Residue Count: 691 
  • Deposited Residue Count: 764 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sorting nexin-5
A, B, C, D
166Mus musculusMutation(s): 0 
Gene Names: Snx5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8U8 (Mus musculus)
Explore Q9D8U8 
Go to UniProtKB:  Q9D8U8
IMPC:  MGI:1916428
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8U8
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inclusion membrane protein EE [auth P],
F [auth Q],
G [auth R],
H [auth S]
25Chlamydia trachomatis D/UW-3/CXMutation(s): 0 
UniProt
Find proteins for P0DJI4 (Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx))
Explore P0DJI4 
Go to UniProtKB:  P0DJI4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJI4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.73α = 90
b = 110.1β = 90.34
c = 86.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesK08 AI091656-04

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description