Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 22806.06 
• Atom Count: 1308 
• Residue Count: 226 
• Unique protein chains: 1

1P9H

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

• DOI: 10.2210/pdb1P9H/pdb

• Classification: CELL ADHESION
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia coli


• Deposited: 2003-05-12 Released: 2004-03-23 
• Deposition Author(s): Nummelin, H., Merckel, M.C., Skurnik, M., Goldman, A.

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Experimental Data Snapshot

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

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

• PubMed: 14765110 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Invasin	A	226	Yersinia enterocolitica	Mutation(s): 0  Gene 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 = 67.050	α = 90.00
b = 67.050	β = 90.00
c = 221.953	γ = 120.00

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-12 
• Released Date: 2004-03-23 
• Deposition Author(s): Nummelin, H., Merckel, M.C., Skurnik, M., Goldman, A.

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