PDBsum entry 7kgo

Immune system

PDB id: 7kgo

Contents

Protein chains

275 a.a.

98 a.a.

Ligands

ILE-LEU-LEU-ASN-LYS-HIS-ILE-ASP-ALA

Metals

_CD

_CL ×3

3NI ×3

Waters ×187

PDB id:

7kgo

Name:

Immune system

Title:

Crystal structure of hla-a 0201In complex with sars-cov-2 n351-359

Structure:

Mhc class i antigen. Chain: a. Engineered: yes. Beta-2-microglobulin. Chain: b. Engineered: yes. Nucleoprotein. Chain: c. Fragment: residues 351-359.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hla-a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: b2m, cdabp0092, hdcma22p. Synthetic: yes. Severe acute respiratory syndrome coronavirus

Resolution:

2.15Å R-factor: 0.185 R-free: 0.229

Authors:

C.Szeto,D.S.M.Chatzileontiadou,A.Riboldi-Tunnicliffe,S.Gras

Key ref:

C.Szeto et al. (2021). The presentation of SARS-CoV-2 peptides by the common HLA-A^∗02:01 molecule. iScience, 24, 102096. PubMed id: 33521593 DOI: 10.1016/j.isci.2021.102096

Date:

18-Oct-20 Release date: 20-Jan-21

Protein chain

Q861F7  (Q861F7_HUMAN) -  MHC class I antigen (Fragment) from Homo sapiens

Seq: 341 a.a.

Struc: 275 a.a.

Protein chain

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 98 a.a.

DOI no: 10.1016/j.isci.2021.102096

iScience 24:102096 (2021)

PubMed id: 33521593

The presentation of SARS-CoV-2 peptides by the common HLA-A^∗02:01 molecule.

C.Szeto, D.S.M.Chatzileontiadou, A.T.Nguyen, H.Sloane, C.A.Lobos, D.Jayasinghe, H.Halim, C.Smith, A.Riboldi-Tunnicliffe, E.J.Grant, S.Gras.

ABSTRACT

CD8+ T cells are crucial for anti-viral immunity; however, understanding T cell responses requires the identification of epitopes presented by human leukocyte antigens (HLA). To date, few SARS-CoV-2-specific CD8+ T cell epitopes have been described. Internal viral proteins are typically more conserved than surface proteins and are often the target of CD8+ T cells. Therefore, we have characterized eight peptides derived from the internal SARS-CoV-2 nucleocapsid protein predicted to bind HLA-A^∗02:01, the most common HLA molecule in the global population. We determined not all peptides could form a complex with HLA-A^∗02:01, and the six crystal structures determined revealed that some peptides adopted a mobile conformation. We therefore provide a molecular understanding of SARS-CoV-2 CD8+ T cell epitopes. Furthermore, we show that there is limited pre-existing CD8+ T cell response toward these epitopes in unexposed individuals. Together, these data show that SARS-CoV-2 nucleocapsid might not contain potent epitopes restricted to HLA-A^∗02:01.