3M18

Crystal structure of variable lymphocyte receptor VLRA.R2.1 in complex with hen egg lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey.

Deng, L.Velikovsky, C.A.Xu, G.Iyer, L.M.Tasumi, S.Kerzic, M.C.Flajnik, M.F.Aravind, L.Pancer, Z.Mariuzza, R.A.

(2010) Proc.Natl.Acad.Sci.USA 107: 13408-13413

  • DOI: 10.1073/pnas.1005475107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adaptive immunity in jawless vertebrates is mediated by leucine-rich repeat proteins called "variable lymphocyte receptors" (VLRs). Two types of VLR (A and B) are expressed by mutually exclusive lymphocyte populations in lamprey. VLRB lymphocytes res ...

    Adaptive immunity in jawless vertebrates is mediated by leucine-rich repeat proteins called "variable lymphocyte receptors" (VLRs). Two types of VLR (A and B) are expressed by mutually exclusive lymphocyte populations in lamprey. VLRB lymphocytes resemble the B cells of jawed vertebrates; VLRA lymphocytes are similar to T cells. We determined the structure of a high-affinity VLRA isolated from lamprey immunized with hen egg white lysozyme (HEL) in unbound and antigen-bound forms. The VLRA-HEL complex demonstrates that certain VLRAs, like gammadelta T-cell receptors (TCRs) but unlike alphabeta TCRs, can recognize antigens directly, without a requirement for processing or antigen-presenting molecules. Thus, these VLRAs feature the nanomolar affinities of antibodies, the direct recognition of unprocessed antigens of both antibodies and gammadelta TCRs, and the exclusive expression on the lymphocyte surface that is unique to alphabeta and gammadelta TCRs.


    Organizational Affiliation

    W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Variable lymphocyte receptor A diversity region
A
251Petromyzon marinusMutation(s): 0 
Find proteins for C7B6Y3 (Petromyzon marinus)
Go to UniProtKB:  C7B6Y3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
B
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.794α = 90.00
b = 68.116β = 110.94
c = 59.751γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance