PXD023487

PXD023487 is an original dataset announced via ProteomeXchange.

Title	Targeted in situ cross-linking for determination of structure and interactions of SARS-CoV-2 proteins in the cellular context
Description	Cross-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.
HostingRepository	PRIDE
AnnounceDate	2021-10-07
AnnouncementXML	Submission_2021-10-07_00:04:07.904.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Moriya Slavin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-08 05:24:18	ID requested
1	2021-10-06 04:32:53	announced
⏵ 2	2021-10-07 00:04:09	announced	2021-10-07: Updated project metadata.

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]

ProteomeXchange project tag: Covid-19

submitter keyword: Mass-Spectrometry, XLMS, SARS-CoV-2, CLMS, HEK293, Nucleocapsid protein,LC-MSMS, Nsp1, Nsp2

Nir Kalisman
contact affiliation	Dept. of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
contact email	nirka@mail.huji.ac.il
lab head
Moriya Slavin
contact affiliation	Biochemistry department in the Hebrew University
contact email	moriya.slavin@mail.huji.ac.il
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/2021/10/PXD023487

PRIDE project URI

• PRIDE
  1. PXD023487
     1. Label: PRIDE project
     2. Name: Targeted in situ cross-linking for determination of structure and interactions of SARS-CoV-2 proteins in the cellular context