3TN0

Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

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Literature

NKT TCR Recognition of CD1d-{alpha}-C-Galactosylceramide.

Patel, O.Cameron, G.Pellicci, D.G.Liu, Z.Byun, H.S.Beddoe, T.McCluskey, J.Franck, R.W.Castano, A.R.Harrak, Y.Llebaria, A.Bittman, R.Porcelli, S.A.Godfrey, D.I.Rossjohn, J.

(2011) J Immunol 187: 4705-4713

  • DOI: 10.4049/jimmunol.1100794
  • Primary Citation of Related Structures:  
    3TN0

  • PubMed Abstract: 
  • NKT cells respond to a variety of CD1d-restricted glycolipid Ags that are structurally related to the prototypic Ag α-galactosylceramide (α-GalCer). A modified analog of α-GalCer with a carbon-based glycosidic linkage (α-C-GalCer) has generated great interest because of its apparent ability to promote prolonged, Th1-biased immune responses ...

    NKT cells respond to a variety of CD1d-restricted glycolipid Ags that are structurally related to the prototypic Ag α-galactosylceramide (α-GalCer). A modified analog of α-GalCer with a carbon-based glycosidic linkage (α-C-GalCer) has generated great interest because of its apparent ability to promote prolonged, Th1-biased immune responses. In this study, we report the activation of spleen NKT cells to α-C-GalCer, and related C-glycoside ligands, is weaker than that of α-GalCer. Furthermore, the Vβ8.2 and Vβ7 NKT TCR affinity for CD1d-α-C-GalCer, and some related analogs, is ∼10-fold lower than that for the NKT TCR-CD1d-α-GalCer interaction. Nevertheless, the crystal structure of the Vβ8.2 NKT TCR-CD1d-α-C-GalCer complex is similar to that of the corresponding NKT TCR-CD1d-α-GalCer complex, although subtle differences at the interface provide a basis for understanding the lower affinity of the NKT TCR-CD1d-α-C-GalCer interaction. Our findings support the concept that for CD1d-restricted NKT cells, altered glycolipid ligands can promote markedly different responses while adopting similar TCR-docking topologies.


    Organizational Affiliation

    Australian Research Council 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1A302Mus musculusMutation(s): 0 
Gene Names: Cd1d1Cd1.1
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: B2mRP23-34E24.5-001mCG_11606
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)C207Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: TRAC
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)D244Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: TRBC1
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Find proteins for P01850 (Homo sapiens)
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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
QUX
Query on QUX

Download Ideal Coordinates CCD File 
F [auth A]N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide
C51 H101 N O8
BNYLLEHBKIGJHB-XHSUSRKPSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
QUX PDBBind:  3TN0 Kd: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.171α = 90
b = 86.368β = 90
c = 236.403γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
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: 2011-12-14
    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