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PXD023487

PXD023487 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTargeted in situ cross-linking for determination of structure and interactions of SARS-CoV-2 proteins in the cellular context
DescriptionCross-linking mass spectrometry (XL-MS) has progressed from studying purified protein assemblies in-vitro towards investigating the same assemblies in intact cells, tissues, and even whole organisms (so called “in situ XL-MS”). In situ XL-MS offers the great advantage of reporting on the architectures of protein complexes as they occur inside cells and tissues. Here we developed a complete workflow of in-situ XL-MS followed by purification, and employ it to investigate SARS-CoV2 protein inside the host cell. We focused on three Sars-Cov-2 proteins for which the structural information is either missing or incomplete: NSP1, NSP2, and the Nucleocapsid protein (N protein). Relatively little is known about the structures of these specific proteins, which was our motivation for choosing them. We were able to identify considerable cross-link sets, of in-situ origin. Integration of the cross-links with additional structural information allowed us to build almost complete models for NSP2 and the N protein.
HostingRepositoryPRIDE
AnnounceDate2021-10-07
AnnouncementXMLSubmission_2021-10-07_00:04:07.904.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMoriya Slavin
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-08 05:24:18ID requested
12021-10-06 04:32:53announced
22021-10-07 00:04:09announced2021-10-07: Updated project metadata.
Publication List
10.1073/PNAS.2103554118;
Slavin M, Zamel J, Zohar K, Eliyahu T, Braitbard M, Brielle E, Baraz L, Stolovich-Rain M, Friedman A, Wolf DG, Rouvinski A, Linial M, Schneidman-Duhovny D, Kalisman N, Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2. Proc Natl Acad Sci U S A, 118(34):(2021) [pubmed]
Keyword List
ProteomeXchange project tag: Covid-19
submitter keyword: Mass-Spectrometry, XLMS, SARS-CoV-2, CLMS, HEK293, Nucleocapsid protein,LC-MSMS, Nsp1, Nsp2
Contact List
Nir Kalisman
contact affiliationDept. of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
contact emailnirka@mail.huji.ac.il
lab head
Moriya Slavin
contact affiliationBiochemistry department in the Hebrew University
contact emailmoriya.slavin@mail.huji.ac.il
dataset submitter
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Dataset FTP location
PRIDE project URI
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