4MO7 | pdb_00004mo7

Crystal structure of superantigen PfiT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.234 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4MO7

This is version 1.1 of the entry. See complete history

Literature

Pfit is a structurally novel Crohn's disease-associated superantigen.

Liu, L.Chen, H.Brecher, M.B.Li, Z.Wei, B.Nandi, B.Zhang, J.Ling, H.Winslow, G.Braun, J.Li, H.

(2013) PLoS Pathog 9: e1003837-e1003837

  • DOI: https://doi.org/10.1371/journal.ppat.1003837
  • Primary Citation Related Structures: 
    4MO7, 4MXM

  • PubMed Abstract: 

    T cell responses to enteric bacteria are important in inflammatory bowel disease. I2, encoded by the pfiT gene of Pseudomonas fluorescens, is a T-cell superantigen associated with human Crohn's disease. Here we report the crystal structure of pfiT at 1.7Å resolution and provide a functional analysis of the interaction of pfiT and its homolog, PA2885, with human class II MHC. Both pfiT and PA2885 bound to mammalian cells and stimulated the proliferation of human lymphocytes. This binding was greatly inhibited by anti-class II MHC HLA-DR antibodies, and to a lesser extent, by anti HLA-DQ and DP antibodies, indicating that the binding was class II MHC-specific. GST-pfiT efficiently precipitated both endogenous and in vitro purified recombinant HLA-DR1 molecules, indicating that pfiT directly interacted with HLA-DR1. Competition studies revealed that pfiT and the superantigen Mycoplasma arthritidis mitogen (MAM) competed for binding to HLA-DR, indicating that their binding sites overlap. Structural analyses established that pfiT belongs to the TetR-family of DNA-binding transcription regulators. The distinct structure of pfiT indicates that it represents a new family of T cell superantigens.


  • Organizational Affiliation
    • Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.

Macromolecule Content 

  • Total Structure Weight: 23.74 kDa 
  • Atom Count: 1,651 
  • Modeled Residue Count: 188 
  • Deposited Residue Count: 212 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator I2212Pseudomonas fluorescens A506Mutation(s): 0 
Gene Names: pfiTPflA506_3695

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.226α = 90
b = 93.661β = 109.82
c = 53.557γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary