3SDX

Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors

Pellicci, D.G.Clarke, A.J.Patel, O.Mallevaey, T.Beddoe, T.Le Nours, J.Uldrich, A.P.McCluskey, J.Besra, G.S.Porcelli, S.A.Gapin, L.Godfrey, D.I.Rossjohn, J.

(2011) Nat Immunol 12: 827-833

  • DOI: 10.1038/ni.2076
  • Primary Citation of Related Structures:  
    3SDA, 3SDC, 3SCM, 3SDX, 3SDD

  • PubMed Abstract: 
  • The most potent foreign antigens for natural killer T cells (NKT cells) are α-linked glycolipids, whereas NKT cell self-reactivity involves weaker recognition of structurally distinct β-linked glycolipid antigens. Here we provide the mechanism for the autoreactivity of T cell antigen receptors (TCRs) on NKT cells to the mono- and tri-glycosylated β-linked agonists β-galactosylceramide (β-GalCer) and isoglobotrihexosylceramide (iGb3), respectively ...

    The most potent foreign antigens for natural killer T cells (NKT cells) are α-linked glycolipids, whereas NKT cell self-reactivity involves weaker recognition of structurally distinct β-linked glycolipid antigens. Here we provide the mechanism for the autoreactivity of T cell antigen receptors (TCRs) on NKT cells to the mono- and tri-glycosylated β-linked agonists β-galactosylceramide (β-GalCer) and isoglobotrihexosylceramide (iGb3), respectively. In binding these disparate antigens, the NKT cell TCRs docked onto CD1d similarly, achieving this by flattening the conformation of the β-linked ligands regardless of the size of the glycosyl head group. Unexpectedly, the antigenicity of iGb3 was attributable to its terminal sugar group making compensatory interactions with CD1d. Thus, the NKT cell TCR molds the β-linked self ligands to resemble the conformation of foreign α-linked ligands, which shows that induced-fit molecular mimicry can underpin the self-reactivity of NKT cell TCRs to β-linked antigens.


    Organizational Affiliation

    Department of Microbiology & Immunology, University of Melbourne, Parkville, Victoria, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1dA, F [auth C]275Homo sapiensMutation(s): 0 
Gene Names: CD1D
Find proteins for P15813 (Homo sapiens)
Explore P15813 
Go to UniProtKB:  P15813
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PHAROS:  P15813
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, G [auth D]99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS:  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NKT TCR Valpha24 chainC [auth E], E [auth G]204Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
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PHAROS:  P01848
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NKT TCR autoreactive-Vbeta11 chainD [auth F], H247Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCY
Query on GCY

Download Ideal Coordinates CCD File 
I [auth A], J [auth C]N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide
C48 H93 N O8
POQRWMRXUOPCLD-HIIAJUEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.041α = 90
b = 152.337β = 97.24
c = 85.119γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release