8BOZ

structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6SS effector/immunity complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Activity and Crystal Structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6SS Effector/Immunity Complex Determined Using an AlphaFold2 Predicted Model.

Le, T.T.H.Kellenberger, C.Boyer, M.Santucci, P.Flaugnatti, N.Cascales, E.Roussel, A.Canaan, S.Journet, L.Cambillau, C.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24021740
  • Primary Citation of Related Structures:  
    8BOZ

  • PubMed Abstract: 

    The type VI secretion system (T6SS) delivers enzymatic effectors into target cells to destroy them. Cells of the same strain protect themselves against effectors with immunity proteins that specifically inhibit effectors. Here, we report the identification and characterization of a Tle3 phospholipase effector and its cognate immunity protein Tli3-an outer membrane lipoprotein from adherent-invasive Escherichia coli (AIEC). Enzymatic assays demonstrate that purified Tle3 AIEC has a phospholipase A1, and not A2, activity and that its toxicity is neutralized by the cognate immunity protein Tli3 AIEC . Tli3 AIEC binds Tle3 in a 1:1 stoichiometric ratio. Tle3 AIEC , Tli3 AIEC and the Tle3 AIEC -Tli3 AIEC complex were purified and subjected to crystallization. The Tle3 AIEC -Tli3 AIEC complex structure could not be solved by SeMet phasing, but only by molecular replacement when using an AlphaFold2 prediction model. Tle3 AIEC exhibits an α/β-hydrolase fold decorated by two protruding segments, including a N-terminus loop. Tli3 AIEC displays a new fold of three stacked β-sheets and a protruding loop that inserts in Tle3 AIEC catalytic crevice. We showed, experimentally, that Tle3 AIEC interacts with the VgrG AIEC cargo protein and AlphaFold2 prediction of the VgrG AIEC -Tle3 AIEC complex reveals a strong interaction between the VgrG AIEC C-terminus adaptor and Tle3 AIEC N-terminal loop.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, Aix Marseille University and CNRS, 13288 Marseille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein658Escherichia coliMutation(s): 0 
Gene Names: FPI65_17315
UniProt
Find proteins for A0A0H2VAD3 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore A0A0H2VAD3 
Go to UniProtKB:  A0A0H2VAD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2VAD3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein274Escherichia coliMutation(s): 0 
Gene Names: FPI65_17310
UniProt
Find proteins for A0A0H2VA42 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore A0A0H2VA42 
Go to UniProtKB:  A0A0H2VA42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2VA42
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.86α = 90
b = 449.07β = 93.18
c = 116.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Refinement description