3NCX | pdb_00003ncx

Crystal structure of EHEC O157:H7 intimin mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.268 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of EHEC Intimin: Insights into the Complementarity between EPEC and EHEC

Yi, Y.Ma, Y.Gao, F.Mao, X.Peng, H.Feng, Y.Fan, Z.Wang, G.Guo, G.Yan, J.Zeng, H.Zou, Q.M.Gao, G.F.

(2010) PLoS One 5: e15285-e15285

  • DOI: https://doi.org/10.1371/journal.pone.0015285
  • Primary Citation Related Structures: 
    3NCW, 3NCX

  • PubMed Abstract: 

    Enterohaemorrhagic E. coli (EHEC) O157:H7 is a primary food-borne bacterial pathogen capable of causing life-threatening human infections which poses a serious challenge to public health worldwide. Intimin, the bacterial outer-membrane protein, plays a key role in the initiating process of EHEC infection. This activity is dependent upon translocation of the intimin receptor (Tir), the intimin binding partner of the bacteria-encoded host cell surface protein. Intimin has attracted considerable attention due to its potential function as an antibacterial drug target. Here, we report the crystal structure of the Tir-binding domain of intimin (Int188) from E. coli O157:H7 at 2.8 Å resolution, together with a mutant (IntN916Y) at 2.6 Å. We also built the structural model of EHEC intimin-Tir complex and analyzed the key binding residues. It suggested that the binding pattern of intimin and Tir between EHEC and Enteropathogenic E. coli (EPEC) adopt a similar mode and they can complement with each other. Detailed structural comparison indicates that there are four major points of structural variations between EHEC and EPEC intimins: one in Domain I (Ig-like domain), the other three located in Domain II (C-type lectin-like domain). These variations result in different binding affinities. These findings provide structural insight into the binding pattern of intimin to Tir and the molecular mechanism of EHEC O157: H7.


  • Organizational Affiliation
    • Department of Clinical Microbiology and Clinical Immunology, College of Medical Laboratory, Third Military Medical University, Chongqing, China.

Macromolecule Content 

  • Total Structure Weight: 41.44 kDa 
  • Atom Count: 3,126 
  • Modeled Residue Count: 371 
  • Deposited Residue Count: 378 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Intimin adherence protein
A, B
189Escherichia coli O157:H7 str. TW14359Mutation(s): 1 
UniProt
Find proteins for P43261 (Escherichia coli O157:H7)
Explore P43261 
Go to UniProtKB:  P43261
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43261
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.268 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.771α = 90
b = 92.488β = 90
c = 100.048γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
PHENIXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary