1YU3

Major Tropism Determinant I1 Variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 

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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major Tropism Determinant (Mtd-I1)
A
381Bordetella phage BPP-1Mutation(s): 0 
Gene Names: mtd
Find proteins for Q775D6 (Bordetella phage BPP-1)
Go to UniProtKB:  Q775D6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 92.308α = 90.00
b = 92.308β = 90.00
c = 102.290γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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