2PO6

Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor.

Borg, N.A.Wun, K.S.Kjer-Nielsen, L.Wilce, M.C.Pellicci, D.G.Koh, R.Besra, G.S.Bharadwaj, M.Godfrey, D.I.McCluskey, J.Rossjohn, J.

(2007) Nature 448: 44-49

  • DOI: 10.1038/nature05907

  • PubMed Abstract: 
  • The CD1 family is a large cluster of non-polymorphic, major histocompatibility complex (MHC) class-I-like molecules that bind distinct lipid-based antigens that are recognized by T cells. The most studied group of T cells that interact with lipid ant ...

    The CD1 family is a large cluster of non-polymorphic, major histocompatibility complex (MHC) class-I-like molecules that bind distinct lipid-based antigens that are recognized by T cells. The most studied group of T cells that interact with lipid antigens are natural killer T (NKT) cells, which characteristically express a semi-invariant T-cell receptor (NKT TCR) that specifically recognizes the CD1 family member, CD1d. NKT-cell-mediated recognition of the CD1d-antigen complex has been implicated in microbial immunity, tumour immunity, autoimmunity and allergy. Here we describe the structure of a human NKT TCR in complex with CD1d bound to the potent NKT-cell agonist alpha-galactosylceramide, the archetypal CD1d-restricted glycolipid. In contrast to T-cell receptor-peptide-antigen-MHC complexes, the NKT TCR docked parallel to, and at the extreme end of the CD1d-binding cleft, which enables a lock-and-key type interaction with the lipid antigen. The structure provides a basis for the interaction between the highly conserved NKT TCR alpha-chain and the CD1d-antigen complex that is typified in innate immunity, and also indicates how variability of the NKT TCR beta-chain can impact on recognition of other CD1d-antigen complexes. These findings provide direct insight into how a T-cell receptor recognizes a lipid-antigen-presenting molecule of the immune system.


    Organizational Affiliation

    The Protein Crystallography Unit, ARC Centre of Excellence in Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1d
A, E
278Homo sapiensMutation(s): 0 
Gene Names: CD1D
Find proteins for P15813 (Homo sapiens)
Go to Gene View: CD1D
Go to UniProtKB:  P15813
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NKT15 alpha-chain
C, G
204Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NKT15 beta-chain
D, H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
AGH
Query on AGH

Download SDF File 
Download CCD File 
C, E
N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 204.012α = 90.00
b = 155.636β = 94.78
c = 85.981γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-25 
  • Released Date: 2007-07-03 
  • Deposition Author(s): Borg, N.A.

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2014-10-29
    Type: Atomic model
  • Version 1.4: 2017-10-18
    Type: Refinement description