4ELM

Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.

Girardi, E.Maricic, I.Wang, J.Mac, T.T.Iyer, P.Kumar, V.Zajonc, D.M.

(2012) Nat Immunol 13: 851-856

  • DOI: 10.1038/ni.2371
  • Primary Citation of Related Structures:  
    4ELK, 4ELM

  • PubMed Abstract: 
  • Glycolipids presented by the major histocompatibility complex (MHC) class I homolog CD1d are recognized by natural killer T cells (NKT cells) characterized by either a semi-invariant T cell antigen receptor (TCR) repertoire (type I NKT cells or iNKT cells) or a relatively variable TCR repertoire (type II NKT cells) ...

    Glycolipids presented by the major histocompatibility complex (MHC) class I homolog CD1d are recognized by natural killer T cells (NKT cells) characterized by either a semi-invariant T cell antigen receptor (TCR) repertoire (type I NKT cells or iNKT cells) or a relatively variable TCR repertoire (type II NKT cells). Here we describe the structure of a type II NKT cell TCR in complex with CD1d-lysosulfatide. Both TCR α-chains and TCR β-chains made contact with the CD1d molecule with a diagonal footprint, typical of MHC-TCR interactions, whereas the antigen was recognized exclusively with a single TCR chain, similar to the iNKT cell TCR. Type II NKT cell TCRs, therefore, recognize CD1d-sulfatide complexes by a distinct recognition mechanism characterized by the TCR-binding features of both iNKT cells and conventional peptide-reactive T cells.


    Organizational Affiliation

    Division of Cell Biology, La Jolla Institute for Allergy & Immunology, La Jolla, California, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1A,
B [auth C]
285Mus musculusMutation(s): 0 
Gene Names: Cd1.1CD1dCd1d1
UniProt
Find proteins for P11609 (Mus musculus)
Explore P11609 
Go to UniProtKB:  P11609
Entity Groups  
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UniProt GroupP11609
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2 microglobulinC [auth B],
D
99Mus musculusMutation(s): 0 
Gene Names: B2mbeta-2-microglobulinmCG_11606RP23-34E24.5-001
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)E, G208Mus musculusMutation(s): 0 
Gene Names: Valpha1 (mouse variable domainhuman constant domain
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hy19.3 TCR beta chain (mouse variable domain, human constant domain)F, H244Mus musculusMutation(s): 0 
Gene Names: Vbeta16 (mouse variable domainhuman constant domain)
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  • Reference Sequence
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-glucopyranoseI 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseJ 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGF
Query on SGF

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth C]
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside
C24 H47 N O10 S
BXSULSOCJNTUJS-YTBMLWRQSA-N
 Ligand Interaction
PLM
Query on PLM

Download Ideal Coordinates CCD File 
N [auth A],
R [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
O [auth C],
P [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.514α = 90
b = 126.996β = 110.53
c = 104.349γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-02-06
    Changes: Non-polymer description
  • Version 1.3: 2015-08-12
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary