4WW1 | pdb_00004ww1

Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8

• PDB DOI: https://doi.org/10.2210/pdb4WW1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-10 Released: 2016-02-03 
• Deposition Author(s): Le Nours, J., Praveena, T., Pellicci, D.G., Lim, R.T., Besra, G., Howell, A.R., Godfrey, D.I., Rossjohn, J., Uldrich, A.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

• PubMed: 26875526 
• DOI: https://doi.org/10.1038/ncomms10570
• Primary Citation Related Structures: 
  4WW1, 4WW2, 4WWK


• 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 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.

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Organizational Affiliation: 
• Infection and Immunity Program &Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.
Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia.
Cancer Immunology Research Program, Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, USA.
Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.94 kDa 
• Atom Count: 3,971 
• Modeled Residue Count: 438 
• Deposited Residue Count: 450 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR Alpha Chain-TRAV21-TRAJ8	A	207	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J279 (Homo sapiens) Explore A0A0B4J279  Go to UniProtKB:  A0A0B4J279
PHAROS:  A0A0B4J279 GTEx:  ENSG00000211801
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848
UniProt Groups	A0A0B4J279P01848

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR Beta Chain-TRBV7-8	B	243	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9  Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.11	α = 90
b = 73.12	β = 94.49
c = 65.6	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Le Nours, J., Praveena, T., Pellicci, D.G., Lim, R.T., Besra, G., Howell, A.R., Godfrey, D.I., Rossjohn, J., Uldrich, A.P.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary