3E6J

Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antigen recognition by variable lymphocyte receptors.

Han, B.W.Herrin, B.R.Cooper, M.D.Wilson, I.A.

(2008) Science 321: 1834-1837

  • DOI: 10.1126/science.1162484

  • PubMed Abstract: 
  • Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required ...

    Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required repertoire for antigen recognition. We have determined a crystal structure for a VLR-antigen complex, VLR RBC36 in complex with the H-antigen trisaccharide from human blood type O erythrocytes, at 1.67 angstrom resolution. RBC36 binds the H-trisaccharide on the concave surface of the LRR modules of the solenoid structure where three key hydrophilic residues, multiple van der Waals interactions, and the highly variable insert of the carboxyl-terminal LRR module determine antigen recognition and specificity. The concave surface assembled from the most highly variable regions of the LRRs, along with diversity in the sequence and length of the highly variable insert, can account for the recognition of diverse antigens by VLRs.


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Variable lymphocyte receptor diversity region
A
229Petromyzon marinusMutation(s): 0 
Gene Names: VLR
Find proteins for Q2VGE8 (Petromyzon marinus)
Go to UniProtKB:  Q2VGE8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DR2
Query on DR2

Download SDF File 
Download CCD File 
A
6-DEOXY-ALPHA-L-IDOPYRANOSYL-(1->2)-ALPHA-D-GLUCOPYRANOSYL-(1->4)-2-(ACETYLAMINO)-2-DEOXY-BETA-L-GULOPYRANOSE
H TYPE II TRISACCHARIDE
C20 H35 N O15
PHTAQVMXYWFMHF-QVPNGJTFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.221α = 90.00
b = 48.564β = 116.51
c = 55.477γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance