PXD050265

PXD050265 is an original dataset announced via ProteomeXchange.

Title	Global population analysis of HLA class I affinity toward proteasome-generated peptides from five main SARS-CoV-2 spike protein RBD variants
Description	Here we report binding index of 305 human HLA class I molecules from 18,771 unique haplotypes of 28,104 individuals to the 821 peptides experimentally observed from spike protein receptor-binding domain (RBD) of 5 main SARS-CoV-2 strains hydrolysed by human proteasomes with constitutive and immuno catalytic phenotypes. Our data read that 4 point mutations in the C-terminal RBD region 496-505 of Omicron B1.1.529 strain results in a dramatic increase of proteasome-mediated release of two public HLA class I epitopes covering 82% and 27% of world population haplotypes. Global population analysis of HLA class I haplotypes specific to these peptides demonstrated decreased mortality of human populations bearing these haplotypes to COVID-19 after but not before December, 2021, when Omicron spread over the world and became dominant SARS-CoV-2 strain. Analysis of population frequency of HLA class I alleles revealed that HLA-B*07:02, -B*08:01, -B*15:01, -C*01:02, -C*06:02 and -C*07:02 potentially provides increased resistance of human population to Omicron. Concluding, we found direct experimental observation, which might be one of the key factors that forced the SARS-CoV-2 virus to cross back the red line of pandemic status.
HostingRepository	PRIDE
AnnounceDate	2025-01-29
AnnouncementXML	Submission_2025-01-29_07:39:25.463.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ivan Butenko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-01 03:11:40	ID requested
⏵ 1	2025-01-29 07:39:25	announced

10.1016/J.ISCI.2025.111873;

submitter keyword: SARS-CoV-2

proteasome

immunoproteasome

HLA class I

IFNγ

Dr. Belogurov
contact affiliation	Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation Scientific Research Instirute for Systems Biology and Medicine, Moscow, Russian Federation
contact email	alexey.belogurov.jr@gmail.com
lab head
Ivan Butenko
contact affiliation	Scientific Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
contact email	ivan.butenko@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/01/PXD050265

PRIDE project URI

• PRIDE
  1. PXD050265
     1. Label: PRIDE project
     2. Name: Global population analysis of HLA class I affinity toward proteasome-generated peptides from five main SARS-CoV-2 spike protein RBD variants