Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 95.47 kDa 
• Atom Count: 7466 
• Modelled Residue Count: 826 
• Deposited Residue Count: 835 
• Unique protein chains: 5

5TEZ

TCR F50 recgonizing M1-HLA-A2

• PDB DOI: 10.2210/pdb5TEZ/pdb

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


• Deposited: 2016-09-23 Released: 2017-09-27 
• Deposition Author(s): Yang, X., Mariuzza, R.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope.

Yang, X., Chen, G., Weng, N.P., Mariuzza, R.A.

(2017) J Biol Chem 292: 18618-18627

• PubMed: 28931605 
• DOI: 10.1074/jbc.M117.810382
• Primary Citation of Related Structures:  
  5TEZ


• PubMed Abstract: 
  

Influenza A virus (IAV) causes an acute infection in humans that is normally eliminated by CD8 ⁺ cytotoxic T lymphocytes. Individuals expressing the MHC class I molecule HLA-A2 produce cytotoxic T lymphocytes bearing T-cell receptors (TCRs) that recognize the immunodominant IAV epitope GILGFVFTL (GIL). Most GIL-specific TCRs utilize α/β chain pairs encoded by the TRAV27/TRBV19 gene combination to recognize this relatively featureless peptide epitope (canonical TCRs). However, ∼40% of GIL-specific TCRs express a wide variety of other TRAV/TRBV combinations (non-canonical TCRs). To investigate the structural underpinnings of this remarkable diversity, we determined the crystal structure of a non-canonical GIL-specific TCR (F50) expressing the TRAV13-1/TRBV27 gene combination bound to GIL-HLA-A2 to 1.7 Å resolution. Comparison of the F50-GIL-HLA-A2 complex with the previously published complex formed by a canonical TCR (JM22) revealed that F50 and JM22 engage GIL-HLA-A2 in markedly different orientations. These orientations are distinguished by crossing angles of TCR to peptide-MHC of 29° for F50 versus 69° for JM22 and by a focus by F50 on the C terminus rather than the center of the MHC α1 helix for JM22. In addition, F50, unlike JM22, uses a tryptophan instead of an arginine to fill a critical notch between GIL and the HLA-A2 α2 helix. The F50-GIL-HLA-A2 complex shows that there are multiple structurally distinct solutions to recognizing an identical peptide-MHC ligand with sufficient affinity to elicit a broad anti-IAV response that protects against viral escape and T-cell clonal loss.

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Organizational Affiliation: 

the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-ILE-LEU-GLY-PHE-VAL-PHE-THR-LEU	A [auth C]	9	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03485  Go to UniProtKB:  P03485

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	B [auth A]	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C [auth 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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR F50 alpha chain	D [auth I]	208	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR F50 beta chain	E [auth J]	243	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.266	α = 90
b = 71.053	β = 96.22
c = 100.693	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-23 
• Released Date: 2017-09-27 
Deposition Author(s): Yang, X., Mariuzza, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI036900

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence