3RUG

Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Literature

A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties

Uldrich, A.P.Patel, O.Cameron, G.Pellicci, D.G.Day, E.B.Sullivan, L.C.Kyparissoudis, K.Kjer-Nielsen, L.Vivian, J.P.Cao, B.Brooks, A.G.Williams, S.J.Illarionov, P.Besra, G.S.Turner, S.J.Porcelli, S.A.McCluskey, J.Smyth, M.J.Rossjohn, J.Godfrey, D.I.

(2011) Nat Immunol 12: 616-623

  • DOI: 10.1038/ni.2051
  • Primary Citation of Related Structures:  
    3AXL, 3RUG

  • PubMed Abstract: 
  • Type I natural killer T cells (NKT cells) are characterized by an invariant variable region 14-joining region 18 (V(α)14-J(α)18) T cell antigen receptor (TCR) α-chain and recognition of the glycolipid α-galactosylceramide (α-GalCer) restricted to the antigen-presenting molecule CD1d ...

    Type I natural killer T cells (NKT cells) are characterized by an invariant variable region 14-joining region 18 (V(α)14-J(α)18) T cell antigen receptor (TCR) α-chain and recognition of the glycolipid α-galactosylceramide (α-GalCer) restricted to the antigen-presenting molecule CD1d. Here we describe a population of α-GalCer-reactive NKT cells that expressed a canonical V(α)10-J(α)50 TCR α-chain, which showed a preference for α-glucosylceramide (α-GlcCer) and bacterial α-glucuronic acid-containing glycolipid antigens. Structurally, despite very limited TCRα sequence identity, the V(α)10 TCR-CD1d-α-GlcCer complex had a docking mode similar to that of type I TCR-CD1d-α-GalCer complexes, although differences at the antigen-binding interface accounted for the altered antigen specificity. Our findings provide new insight into the structural basis and evolution of glycolipid antigen recognition and have notable implications for the scope and immunological role of glycolipid-specific T cell responses.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1A, C302Mus musculusMutation(s): 0 
Gene Names: Cd1d1Cd1.1
UniProt
Find proteins for P11609 (Mus musculus)
Explore P11609 
Go to UniProtKB:  P11609
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UniProt GroupP11609
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, D99Mus 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Valpha10(mouse variable domain, human constant domain)E, G204Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Vbeta8.1(mouse variable domain, human constant domain)F, H241Mus musculusMutation(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-glucopyranoseI, J 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DB6
Query on DB6

Download Ideal Coordinates CCD File 
K [auth A],
N [auth C]
(11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide
C44 H83 N O9
WSXMIFGRYXQZQZ-IHVNXUITSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
O [auth C],
P [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DB6 Binding MOAD:  3RUG Kd: 4400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.14α = 90
b = 118.834β = 110.24
c = 108.125γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
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: 2011-08-03
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary