3SDD

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

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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:  
    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 ...

    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 CD1d1A302Mus musculusMutation(s): 0 
Gene Names: Cd1.1, Cd1d1
UniProt
Find proteins for P11609 (Mus musculus)
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Go to UniProtKB:  P11609
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UniProt GroupP11609
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NKT TCR Valpha14 chainC207Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NKT TCR autoreactive-Vbeta6 chainD245Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3GD
Query on 3GD
Download Ideal Coordinates CCD File 
H [auth A]N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide
C52 H99 N O13
QYWVASPEUXEHSY-NNRNTGNWSA-N		 Ligand Interaction
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		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3GD PDBBind:  3SDD Kd: 4840 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.469α = 90
b = 94.469β = 90
c = 291.063γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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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