1P9H

CRYSTAL STRUCTURE OF THE COLLAGEN-BINDING DOMAIN OF YERSINIA ADHESIN YadA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll.

Nummelin, H.Merckel, M.C.Leo, J.C.Lankinen, H.Skurnik, M.Goldman, A.

(2004) Embo J. 23: 701-711

  • DOI: 10.1038/sj.emboj.7600100

  • PubMed Abstract: 
  • The crystal structure of the recombinant collagen-binding domain of Yersinia adhesin YadA from Yersinia enterocolitica serotype O:3 was solved at 1.55 A resolution. The trimeric structure is composed of head and neck regions, and the collagen binding ...

    The crystal structure of the recombinant collagen-binding domain of Yersinia adhesin YadA from Yersinia enterocolitica serotype O:3 was solved at 1.55 A resolution. The trimeric structure is composed of head and neck regions, and the collagen binding head region is a novel nine-coiled left-handed parallel beta-roll. Before the beta-roll, the polypeptide loops from one monomer to the rest, and after the beta-roll the neck region does the same, making the transition from the globular head region to the narrower stalk domain. This creates an intrinsically stable 'lock nut' structure. The trimeric form of YadA is required for collagen binding, and mutagenesis of its surface residues allowed identification of a putative collagen-binding surface. Furthermore, a new structure-sequence motif for YadA beta-roll was used to identify putative YadA-head-like domains in a variety of human and plant pathogens. Such domains may therefore be a common bacterial strategy for avoiding host response.


    Organizational Affiliation

    Macromolecular X-ray Crystallography Group, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Invasin
A
226Yersinia enterocoliticaGene Names: yadA (invA, yop1, yopA)
Find proteins for P31489 (Yersinia enterocolitica)
Go to UniProtKB:  P31489
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 67.050α = 90.00
b = 67.050β = 90.00
c = 221.953γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance