4WWK

Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.

Le Nours, J.Praveena, T.Pellicci, D.G.Gherardin, N.A.Ross, F.J.Lim, R.T.Besra, G.S.Keshipeddy, S.Richardson, S.K.Howell, A.R.Gras, S.Godfrey, D.I.Rossjohn, J.Uldrich, A.P.

(2016) Nat Commun 7: 10570-10570

  • DOI: 10.1038/ncomms10570
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crucial to Natural Killer T (NKT) cell function is the interaction between their T-cell receptor (TCR) and CD1d-antigen complex. However, the diversity of the NKT cell repertoire and the ensuing interactions with CD1d-antigen remain unclear. We descr ...

    Crucial to Natural Killer T (NKT) cell function is the interaction between their T-cell receptor (TCR) and CD1d-antigen complex. However, the diversity of the NKT cell repertoire and the ensuing interactions with CD1d-antigen remain unclear. We describe an atypical population of CD1d-α-galactosylceramide (α-GalCer)-reactive human NKT cells that differ markedly from the prototypical TRAV10-TRAJ18-TRBV25-1(+) type I NKT cell repertoire. These cells express a range of TCR α- and β-chains that show differential recognition of glycolipid antigens. Two atypical NKT TCRs (TRAV21-TRAJ8-TRBV7-8 and TRAV12-3-TRAJ27-TRBV6-5) bind orthogonally over the A'-pocket of CD1d, adopting distinct docking modes that contrast with the docking mode of all type I NKT TCR-CD1d-antigen complexes. Moreover, the interactions with α-GalCer differ between the type I and these atypical NKT TCRs. Accordingly, diverse NKT TCR repertoire usage manifests in varied docking strategies and specificities towards CD1d-α-GalCer and related antigens, thus providing far greater scope for diverse glycolipid antigen recognition.


    Organizational Affiliation

    Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TCR Alpha Chain-TRAV12-3
A
209Homo sapiensMutation(s): 0 
Gene Names: TRACTCRATRAV12-3
Find proteins for A0A0B4J271 (Homo sapiens)
Go to UniProtKB:  A0A0B4J271
NIH Common Fund Data Resources
PHAROS  A0A0B4J271
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS  P01848

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TCR Beta Chain-TRBV6-5
B
243Homo sapiensMutation(s): 0 
Gene Names: TRBV6-5TRBC2TCRBC2
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
NIH Common Fund Data Resources
PHAROS  A0A5B9
Find proteins for A0A0K0K1A5 (Homo sapiens)
Go to UniProtKB:  A0A0K0K1A5
NIH Common Fund Data Resources
PHAROS  A0A0K0K1A5

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d
C
278Homo sapiensMutation(s): 0 
Gene Names: CD1D
Find proteins for P15813 (Homo sapiens)
Go to UniProtKB:  P15813
NIH Common Fund Data Resources
PHAROS  P15813

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
D
119Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JLS
Query on JLS

Download CCD File 
C
(15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide
C48 H93 N O9
QMLKBWVXCMTWOZ-WWHSRKRPSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.38α = 90
b = 76.07β = 90
c = 255.72γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence