6MSS

Diversity in the type II Natural Killer T cell receptor repertoire and antigen specificity leads to differing CD1d docking strategies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors.

Almeida, C.F.Sundararaj, S.Le Nours, J.Praveena, T.Cao, B.Burugupalli, S.Smith, D.G.M.Patel, O.Brigl, M.Pellicci, D.G.Williams, S.J.Uldrich, A.P.Godfrey, D.I.Rossjohn, J.

(2019) Nat Commun 10: 5242-5242

  • DOI: 10.1038/s41467-019-12941-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Type I and type II natural killer T (NKT) cells are restricted to the lipid antigen-presenting molecule CD1d. While we have an understanding of the antigen reactivity and function of type I NKT cells, our knowledge of type II NKT cells in health and ...

    Type I and type II natural killer T (NKT) cells are restricted to the lipid antigen-presenting molecule CD1d. While we have an understanding of the antigen reactivity and function of type I NKT cells, our knowledge of type II NKT cells in health and disease remains unclear. Here we describe a population of type II NKT cells that recognise and respond to the microbial antigen, α-glucuronosyl-diacylglycerol (α-GlcADAG) presented by CD1d, but not the prototypical type I NKT cell agonist, α-galactosylceramide. Surprisingly, the crystal structure of a type II NKT TCR-CD1d-α-GlcADAG complex reveals a CD1d F'-pocket-docking mode that contrasts sharply with the previously determined A'-roof positioning of a sulfatide-reactive type II NKT TCR. Our data also suggest that diverse type II NKT TCRs directed against distinct microbial or mammalian lipid antigens adopt multiple recognition strategies on CD1d, thereby maximising the potential for type II NKT cells to detect different lipid antigens.


    Organizational Affiliation

    Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia.,School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC, 3010, Australia. auldrich@unimelb.edu.au.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia. auldrich@unimelb.edu.au.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia. godfrey@unimelb.edu.au.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC, 3010, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC, 3010, Australia. godfrey@unimelb.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A11B8.2 NKT TCR alpha-chain
A
203N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A11B8.2 NKT TCR beta-chain
B
245N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
C
302Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
D
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRV
Query on SRV

Download SDF File 
Download CCD File 
C
(2S)-2-(heptadecanoyloxy)-3-{[(10S)-10-methyloctadecanoyl]oxy}propyl alpha-D-glucopyranosiduronic acid
C45 H84 O11
GTQHUJVSZUDBBM-ASILJYLZSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.580α = 90.00
b = 141.260β = 90.00
c = 170.670γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references