2YKT

Crystal structure of the I-BAR domain of IRSp53 (BAIAP2) in complex with an EHEC derived Tir peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Complex Formation between Human Irsp53 and the Translocated Intimin Receptor Tir of Enterohemorrhagic E. Coli.

De Groot, J.C.Schluter, K.Carius, Y.Quedenau, C.Vingadassalom, D.Faix, J.Weiss, S.M.Reichelt, J.Standfuss-Gabisch, C.Lesser, C.F.Leong, J.M.Heinz, D.W.Bussow, K.Stradal, T.E.B.

(2011) Structure 19: 1294

  • DOI: https://doi.org/10.1016/j.str.2011.06.015
  • Primary Citation of Related Structures:  
    2YKT

  • PubMed Abstract: 

    Actin assembly beneath enterohemorrhagic E. coli (EHEC) attached to its host cell is triggered by the intracellular interaction of its translocated effector proteins Tir and EspF(U) with human IRSp53 family proteins and N-WASP. Here, we report the structure of the N-terminal I-BAR domain of IRSp53 in complex with a Tir-derived peptide, in which the homodimeric I-BAR domain binds two Tir molecules aligned in parallel. This arrangement provides a protein scaffold linking the bacterium to the host cell's actin polymerization machinery. The structure uncovers a specific peptide-binding site on the I-BAR surface, conserved between IRSp53 and IRTKS. The Tir Asn-Pro-Tyr (NPY) motif, essential for pedestal formation, is specifically recognized by this binding site. The site was confirmed by mutagenesis and in vivo-binding assays. It is possible that IRSp53 utilizes the NPY-binding site for additional interactions with as yet unknown partners within the host cell.


  • Organizational Affiliation

    Division of Structural Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 1-ASSOCIATED PROTEIN 2253Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQB8 (Homo sapiens)
Explore Q9UQB8 
Go to UniProtKB:  Q9UQB8
PHAROS:  Q9UQB8
GTEx:  ENSG00000175866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQB8
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSLOCATED INTIMIN RECEPTOR PROTEIN13Escherichia coli O157:H7 str. TW14359Mutation(s): 0 
UniProt
Find proteins for C6UYL8 (Escherichia coli O157:H7 (strain TW14359 / EHEC))
Explore C6UYL8 
Go to UniProtKB:  C6UYL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6UYL8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.354α = 90
b = 187.362β = 90
c = 36.806γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description