3SDC

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-globotrihexosylceramide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1038/ni.2076
  • Primary Citation of Related Structures:  
    3SCM, 3SDA, 3SDC, 3SDD, 3SDX

  • 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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1302Mus musculusMutation(s): 0 
Gene Names: Cd1.1Cd1d1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus)
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Go to UniProtKB:  P11609
IMPC:  MGI:107674
Entity Groups  
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UniProt GroupP11609
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NKT TCR Valpha14 chain207Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
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Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NKT TCR autoreactive-Vbeta6 chain245Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3GB
Query on 3GB

Download Ideal Coordinates CCD File 
H [auth A]N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide
C62 H117 N O18
YWHNDSBMLSKIRV-MMYBRHQRSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3GB PDBBind:  3SDC Kd: 1.07e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.35α = 90
b = 94.35β = 90
c = 287.86γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary