PXD063489

PXD063489 is an original dataset announced via ProteomeXchange.

Title	Atypical features of cetacean coronavirus spikes highlight structural plasticity of the S glycoprotein
Description	Coronaviruses (CoVs) exhibit a remarkable ability for spill-over infections into naive host populations. While much research has focused on the spike (S) glycoproteins of zoonotic alpha- and betacoronaviruses, the S proteins of gamma- and deltacoronaviruses, which predominantly infect avian hosts, remain poorly understood. Here, we present high-resolution cryo-EM structures of S proteins from two distinct gammacoronaviruses (75.7% sequence identity) that atypically infect marine mammals and belong to the Gammacoronavirus delphinapteri species. The cryo-EM reconstructions reveal that the spikes exhibit a unique quaternary architecture that distinguishes them from other coronaviruses. The S protein features a previously unidentified, tripodal quaternary assembly of the S1 subunit, in which S1B domains are presented in an upright position while their putative receptor binding sites are shielded by extended loops from the S1A domain of the same protomers. Additionally, the CeCoV spike proteins have evolved an additional and unique ~200 residue N-terminal domain (S10). S10 lacks homology to known protein sequences but displays structural similarity to the cupin protein superfamily. This represents a remarkable case of coronaviral exaptation of a host protein integrated into the S glycoprotein. Moreover, glycoproteomic analyses reveal that CeCoV S proteins are extensively N-glycosylated (>100 N-glycans per trimer), with a notable abundance of high-mannose glycans on S10 and novel O-glycosylation sites within a mucin-like loop at the trimer apex, all contributing to a dense glycan shield, potentially masking immunogenic epitopes. These findings demonstrate the structural diversity and adaptability of CoV S proteins, including alternative quaternary assemblies, additional domains, and diverse glycosylation strategies, offering new insights into the evolutionary mechanisms that enable coronaviruses to expand their host range and establish infections in novel species.
HostingRepository	PRIDE
AnnounceDate	2026-03-03
AnnouncementXML	Submission_2026-03-03_04:27:31.298.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tatiana Shamorkina
SpeciesList	scientific name: Cetacea; NCBI TaxID: NEWT:9721;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-30 02:54:28	ID requested
⏵ 1	2026-03-03 04:27:31	announced

10.1371/JOURNAL.PPAT.1013855;

submitter keyword: Coronavirus, Glycoproteomics, Cetacean, coronavirus_spike

Joost Snijder
contact affiliation	Biomolecular Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
contact email	j.snijder@uu.nl
lab head
Tatiana Shamorkina
contact affiliation	Utrecht University
contact email	t.m.shamorkina@uu.nl
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/2026/03/PXD063489

PRIDE project URI

• PRIDE
  1. PXD063489
     1. Label: PRIDE project
     2. Name: Atypical features of cetacean coronavirus spikes highlight structural plasticity of the S glycoprotein