7EA6 | pdb_00007ea6

Crystal structure of TCR-017 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb7EA6/pdb

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


• Deposited: 2021-03-06 Released: 2021-10-13 
• Deposition Author(s): Nagae, M., Yamasaki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Identification of conserved SARS-CoV-2 spike epitopes that expand public cTfh clonotypes in mild COVID-19 patients.

Lu, X., Hosono, Y., Nagae, M., Ishizuka, S., Ishikawa, E., Motooka, D., Ozaki, Y., Sax, N., Maeda, Y., Kato, Y., Morita, T., Shinnakasu, R., Inoue, T., Onodera, T., Matsumura, T., Shinkai, M., Sato, T., Nakamura, S., Mori, S., Kanda, T., Nakayama, E.E., Shioda, T., Kurosaki, T., Takeda, K., Kumanogoh, A., Arase, H., Nakagami, H., Yamashita, K., Takahashi, Y., Yamasaki, S.

(2021) J Exp Medicine 218

• PubMed: 34647971 
• DOI: https://doi.org/10.1084/jem.20211327
• Primary Citation Related Structures: 
  7EA6


• PubMed Abstract: 
  

  Adaptive immunity is a fundamental component in controlling COVID-19. In this process, follicular helper T (Tfh) cells are a subset of CD4+ T cells that mediate the production of protective antibodies; however, the SARS-CoV-2 epitopes activating Tfh cells are not well characterized. Here, we identified and crystallized TCRs of public circulating Tfh (cTfh) clonotypes that are expanded in patients who have recovered from mild symptoms. These public clonotypes recognized the SARS-CoV-2 spike (S) epitopes conserved across emerging variants. The epitope of the most prevalent cTfh clonotype, S864-882, was presented by multiple HLAs and activated T cells in most healthy donors, suggesting that this S region is a universal T cell epitope useful for booster antigen. SARS-CoV-2-specific public cTfh clonotypes also cross-reacted with specific commensal bacteria. In this study, we identified conserved SARS-CoV-2 S epitopes that activate public cTfh clonotypes associated with mild symptoms.

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Organizational Affiliation: 
• Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan.
Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan.
Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
KOTAI Biotechnologies, Inc., Suita, Japan.
Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan.
Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan.
Laboratory of Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Suita, Japan.
Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.
Tokyo Shinagawa Hospital, Tokyo, Japan.
Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
Laboratory of Immunochemistry, Immunology Frontier Research Center, Osaka University, Suita, Japan.
Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan.
Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
Laboratory of Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Department of Mucosal Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan.
Department of Health Development and Medicine, Graduate School of Medicine, Osaka University, Suita, Japan.
Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan.
Division of Molecular Design, Research Center for Systems Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 99.3 kDa 
• Atom Count: 7,161 
• Modeled Residue Count: 865 
• Deposited Residue Count: 880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor 017 alpha chain	A [auth D], C [auth A]	201	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor 017 beta chain	B [auth E], D [auth B]	239	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.049	α = 90
b = 81.175	β = 90
c = 315.105	γ = 90

Software Package:

Software Name	Purpose
PHENIX	data reduction
PHENIX	refinement
Coot	model building
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Nagae, M., Yamasaki, S.

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary