7F4W

Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4

Summary for 7F4W

• Entry DOI: 10.2210/pdb7f4w/pdb
• Descriptor: MHC class I antigen, Beta-2-microglobulin, SARS-CoV-2 T-cell Epitope pep4 (3 entities in total)
• Functional Keywords: mhc, hla, sars-cov-2, epitope, immune system
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 6
• Total formula weight: 97594.14

Authors

Deng, S.,Jin, T. (deposition date: 2021-06-21, release date: 2021-08-25, Last modification date: 2024-10-16)

Primary citation

Zhang, H.,Deng, S.,Ren, L.,Zheng, P.,Hu, X.,Jin, T.,Tan, X.
Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.
Cell Rep, 36:109708-109708, 2021

PubMed Abstract: Cellular immunity is important in determining the disease severity of COVID-19 patients. However, current understanding of SARS-CoV-2 epitopes mediating cellular immunity is limited. Here we apply T-Scan, a recently developed method, to identify CD8 T cell epitopes from COVID-19 patients of four major HLA-A alleles. Several identified epitopes are conserved across human coronaviruses, which might mediate pre-existing cellular immunity to SARS-CoV-2. In addition, we identify and validate four epitopes that were mutated in the newly circulating variants, including the Delta variant. The mutations significantly reduce T cell responses to the epitope peptides in convalescent and vaccinated samples. We further determine the crystal structure of HLA-A02:01/HLA-A24:02 in complex with the epitope KIA_S/NYN_S, respectively, which reveals the importance of K417 and L452 of the spike protein for binding to HLA. Our data suggest that evading cellular immunity might contribute to the increased transmissibility and disease severity associated with the new SARS-CoV-2 variants.

PubMed: 34506741
DOI: 10.1016/j.celrep.2021.109708

Experimental method

X-RAY DIFFRACTION (2.9 Å)