7JWI | pdb_00007jwi

Crystal structure of B17.R2 TCR in complex with H2D-b-NP366

• PDB DOI: https://doi.org/10.2210/pdb7JWI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens, Influenza A virus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-25 Released: 2021-07-07 
• Deposition Author(s): Farenc, C., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.281 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.250 (DCC) 

Starting Model: experimental

Literature

Canonical T cell receptor docking on peptide-MHC is essential for T cell signaling.

Zareie, P., Szeto, C., Farenc, C., Gunasinghe, S.D., Kolawole, E.M., Nguyen, A., Blyth, C., Sng, X.Y.X., Li, J., Jones, C.M., Fulcher, A.J., Jacobs, J.R., Wei, Q., Wojciech, L., Petersen, J., Gascoigne, N.R.J., Evavold, B.D., Gaus, K., Gras, S., Rossjohn, J., La Gruta, N.L.

(2021) Science 372

• PubMed: 34083463 
• DOI: https://doi.org/10.1126/science.abe9124
• Primary Citation Related Structures: 
  7JWI, 7JWJ


• PubMed Abstract: 
  

  T cell receptor (TCR) recognition of peptide-major histocompatibility complexes (pMHCs) is characterized by a highly conserved docking polarity. Whether this polarity is driven by recognition or signaling constraints remains unclear. Using "reversed-docking" TCRβ-variable (TRBV) 17 ⁺ TCRs from the naïve mouse CD8 ⁺ T cell repertoire that recognizes the H-2D ^b -NP ₃₆₆ epitope, we demonstrate that their inability to support T cell activation and in vivo recruitment is a direct consequence of reversed docking polarity and not TCR-pMHCI binding or clustering characteristics. Canonical TCR-pMHCI docking optimally localizes CD8/Lck to the CD3 complex, which is prevented by reversed TCR-pMHCI polarity. The requirement for canonical docking was circumvented by dissociating Lck from CD8. Thus, the consensus TCR-pMHC docking topology is mandated by T cell signaling constraints.

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Organizational Affiliation: 
• Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Science and the ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, New South Wales, Australia.
Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Monash Micro Imaging, Monash University, Clayton, Victoria, Australia.
Immunology Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545.
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.
Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail] [e-mail] [e-mail].
Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 104.84 kDa 
• Atom Count: 6,864 
• Modeled Residue Count: 828 
• Deposited Residue Count: 921 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A	362	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus) Explore P01899  Go to UniProtKB:  P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	C	9	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0U8  Go to UniProtKB:  Q9Q0U8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
B17.R2 TCR alpha chain	D	207	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
B17.R2 TCR beta chain	E	243	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.281 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.250 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.668	α = 90
b = 140.997	β = 90
c = 217.649	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XFIT	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Farenc, C., Rossjohn, J.

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary