PXD058750
PXD058750 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein |
| Description | The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigated how mutations and a deletion in the KP.3.1.1 spike protein (S) affect ACE2 binding and antibody escape. Mass spectrometry revealed a new glycan site at residue N30 and altered glycoforms at neighboring N61. Cryo-EM structures showed that the N30 glycan and rearrangement of adjacent residues did not significantly change the overall spike structure, up-down ratio of the receptor-binding domains (RBDs), or ACE2 binding. Furthermore, a KP.3.1.1 S structure with hACE2 further confirmed an epistatic effect between F456L and Q493E on ACE2 binding. Our analysis shows SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-06-07 |
| AnnouncementXML | Submission_2025-06-07_17:57:31.085.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Sabyasachi Baboo |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: SARS coronavirus; NCBI TaxID: 227859; |
| ModificationList | HexNAc; Deamidated:18O(1); Oxidation; Gln->pyro-Glu |
| Instrument | Orbitrap Eclipse |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-12-10 18:06:54 | ID requested | |
| ⏵ 1 | 2025-06-07 17:57:31 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: SARS-CoV-2, COVID-19, KP.3.1.1, hACE2, N-glycosylation, DeGlyPHER, DatasetType:Proteomics |
Contact List
| John R. Yates III | |
|---|---|
| contact affiliation | The Scripps Research Institute |
| contact email | jyates@scripps.edu |
| lab head | |
| Sabyasachi Baboo | |
| contact affiliation | The Scripps Research Institute, La Jolla, CA |
| contact email | sbaboo@scripps.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive-ftp.ucsd.edu/v07/MSV000096635/ |
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