2IOU

Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella brochiseptica Virulence Factor Pertactin extracellular domain (Prn-E).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Selective Ligand Recognition by a Diversity-Generating Retroelement Variable Protein

Miller, J.L.Le Coq, J.Hodes, A.Barbalat, R.Miller, J.F.Ghosh, P.

(2008) PLoS Biol 6: e131-e131

  • DOI: 10.1371/journal.pbio.0060131
  • Primary Citation of Related Structures:  
    2IOU

  • PubMed Abstract: 
  • Diversity-generating retroelements (DGRs) recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd) bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd ...

    Diversity-generating retroelements (DGRs) recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd) bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd. Despite large dissimilarities in ligand binding mode, principles underlying selective recognition were strikingly conserved between Mtd and immunoreceptors. Central to this was the differential amplification of binding strengths by avidity (i.e., multivalency), which not only relaxed the demand for optimal complementarity between Mtd and pertactin but also enhanced distinctions among binding events to provide selectivity. A quantitatively similar balance between complementarity and avidity was observed for Bordetella bacteriophage DGR as occurs in the immune system, suggesting that variable repertoires operate under a narrow set of conditions to recognize novel ligands.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major Tropism Determinant P1A, B, C, D, E, F376Bordetella virus BPP1Mutation(s): 0 
Gene Names: mtd
UniProt
Find proteins for Q775D6 (Bordetella phage BPP-1)
Explore Q775D6 
Go to UniProtKB:  Q775D6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pertactin Extracellular DomainG, H535Bordetella bronchiseptica RB50Mutation(s): 0 
Gene Names: Prn
UniProt
Find proteins for Q3YE50 (Bordetella bronchiseptica)
Explore Q3YE50 
Go to UniProtKB:  Q3YE50
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 413.464α = 90
b = 413.464β = 90
c = 98.859γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Advisory, Refinement description