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 

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

  • 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. He ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major Tropism Determinant P1
A, B, C, D, E, F
376Bordetella phage BPP-1Mutation(s): 0 
Gene Names: mtd
Find proteins for Q775D6 (Bordetella phage BPP-1)
Go to UniProtKB:  Q775D6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pertactin Extracellular Domain
G, H
535Bordetella bronchisepticaMutation(s): 0 
Find proteins for Q3YE50 (Bordetella bronchiseptica)
Go to UniProtKB:  Q3YE50
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 413.464α = 90.00
b = 413.464β = 90.00
c = 98.859γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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