PXD039583 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Glycosite mapping and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE |
Description | Mucin-domain glycoproteins are densely O-glycosylated and play key roles in a host of biological functions. In particular, the T-cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, 3, 4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans, which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamic (MD) simulations of TIM-3 and 4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome. |
HostingRepository | PRIDE |
AnnounceDate | 2023-09-27 |
AnnouncementXML | Submission_2023-09-27_12:35:02.754.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | AlexandraSteigmeyer |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; O-glycosylated residue; deamidated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Eclipse |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-01-20 03:33:18 | ID requested | |
⏵ 1 | 2023-09-27 12:35:03 | announced | |
2 | 2023-11-14 08:28:29 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
submitter keyword: O-glycoprotein, TIM-1, cancer, mucinase, TIM-4, TIM-3, O-glycosylation, immune checkpoint, T-cell immunoglobulin and mucin-domain containing, LC-MS/MS, molecular dynamics, mucinome,mucin, O-glycoproteomics, mucin domain, checkpoint inhibitor, O-glycoprotease |
Contact List
Stacy A.Malaker |
contact affiliation | Department of Chemistry, Yale University, New Haven, CT 06511, USA |
contact email | stacy.malaker@yale.edu |
lab head | |
AlexandraSteigmeyer |
contact affiliation | Yale University, Department of Chemistry |
contact email | alexandra.steigmeyer@yale.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039583
- Label: PRIDE project
- Name: Glycosite mapping and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE