1YU0

Major Tropism Determinant P1 Variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The C-type lectin fold as an evolutionary solution for massive sequence variation

McMahon, S.A.Miller, J.L.Lawton, J.A.Kerkow, D.E.Hodes, A.Marti-Renom, M.A.Doulatov, S.Narayanan, E.Sali, A.Miller, J.F.Ghosh, P.

(2005) Nat Struct Mol Biol 12: 886-892

  • DOI: 10.1038/nsmb992
  • Primary Citation of Related Structures:  
    1YU4, 1YU3, 1YU2, 1YU1, 1YU0

  • PubMed Abstract: 
  • Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage ...

    Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage. Variation in Mtd, with its approximately 10(13) possible sequences, enables phage adaptation to Bordetella spp. Mtd is an intertwined, pyramid-shaped trimer, with variable residues organized by its CLec fold into discrete receptor-binding sites. The CLec fold provides a highly static scaffold for combinatorial display of variable residues, probably reflecting a different evolutionary solution for balancing diversity against stability from that in the immunoglobulin fold. Mtd variants are biased toward the receptor pertactin, and there is evidence that the CLec fold is used broadly for sequence variation by related retroelements.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major Tropism Determinant (Mtd-P1)A381Bordetella 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.128 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.258α = 90
b = 92.258β = 90
c = 102.231γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance