3AXL | pdb_00003axl

Murine Valpha 10 Vbeta 8.1 T-cell receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.327 (Depositor), 0.306 (DCC) 
  • R-Value Work: 
    0.254 (Depositor) 
  • R-Value Observed: 
    0.258 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3AXL

This is version 1.1 of the entry. See complete history

Literature

A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties

Uldrich, A.P.Patel, O.Cameron, G.Pellicci, D.G.Day, E.B.Sullivan, L.C.Kyparissoudis, K.Kjer-Nielsen, L.Vivian, J.P.Cao, B.Brooks, A.G.Williams, S.J.Illarionov, P.Besra, G.S.Turner, S.J.Porcelli, S.A.McCluskey, J.Smyth, M.J.Rossjohn, J.Godfrey, D.I.

(2011) Nat Immunol 12: 616-623

  • DOI: https://doi.org/10.1038/ni.2051
  • Primary Citation Related Structures: 
    3AXL, 3RUG

  • PubMed Abstract: 

    Type I natural killer T cells (NKT cells) are characterized by an invariant variable region 14-joining region 18 (V(α)14-J(α)18) T cell antigen receptor (TCR) α-chain and recognition of the glycolipid α-galactosylceramide (α-GalCer) restricted to the antigen-presenting molecule CD1d. Here we describe a population of α-GalCer-reactive NKT cells that expressed a canonical V(α)10-J(α)50 TCR α-chain, which showed a preference for α-glucosylceramide (α-GlcCer) and bacterial α-glucuronic acid-containing glycolipid antigens. Structurally, despite very limited TCRα sequence identity, the V(α)10 TCR-CD1d-α-GlcCer complex had a docking mode similar to that of type I TCR-CD1d-α-GalCer complexes, although differences at the antigen-binding interface accounted for the altered antigen specificity. Our findings provide new insight into the structural basis and evolution of glycolipid antigen recognition and have notable implications for the scope and immunological role of glycolipid-specific T cell responses.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia.

Macromolecule Content 

  • Total Structure Weight: 97 kDa 
  • Atom Count: 6,728 
  • Modeled Residue Count: 849 
  • Deposited Residue Count: 872 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Valpha 10A,
C [auth G]
198Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vbeta 8.1B,
D [auth H]
238Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.327 (Depositor), 0.306 (DCC) 
  • R-Value Work:  0.254 (Depositor) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.841α = 90
b = 65.801β = 97.14
c = 97.375γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Refinement description, Structure summary