Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

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

Macromolecule Content

• Total Structure Weight: 95473.13 
• Atom Count: 6661 
• Residue Count: 835 
• Unique protein chains: 5

5TEZ

TCR F50 recgonizing M1-HLA-A2

• DOI: 10.2210/pdb5TEZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Influenza A virus (strain A/Puerto Rico/8/1934 H1N1), Homo sapiens
• Expression System: Escherichia coli


• 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 

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 

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


• 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.

---

Organizational Affiliation: 

From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, A-2 alpha chain	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens) Go to Gene View: HLA-A Go to UniProtKB:  P01892

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
TCR F50 alpha chain	I	208	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
TCR F50 beta chain	J	243	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 66.266	α = 90.00
b = 71.053	β = 96.22
c = 100.693	γ = 90.00

Software Package:

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

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.

---

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

Revision History 

• Version 1.0: 2017-09-27
  Type: Initial release
• Version 1.1: 2017-10-04
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Database references