PXD025391

PXD025391 is an original dataset announced via ProteomeXchange.

Title	A3G-Vif-CBFB-CRL5 Cross-Linking with DSSO
Description	Here we use an optimization cross-linking mass spectrometry (XL-MS) pipeline for the structural characterization of a dynamic HIV-host protein complex. Using DSSO-based XL-MS analysis, residue-protein proximity restraints based on functional genetics, and integrative modeling, we define the structure of the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFβ). Using a XL-MS3 methodology, we identify 132 inter-linked peptides and integrate the data with atomic structures of the subunits and mutagenesis data, and computed an integrative structure model of the heptameric A3G-CRL5-Vif-CBFβ complex. The resulting model ensemble quantifies the dynamic heterogenity of the A3G C-terminal domain, as well as CUL5 flexibility, and defines the interface between Vif and A3G. Our model can be used to rationalize previous structural, mutatagenesis, and functional data not included in modeling. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes and provides new visualization tools for characterizing cross-linking data.
HostingRepository	PRIDE
AnnounceDate	2021-11-03
AnnouncementXML	Submission_2021-11-03_03:00:10.458.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Robyn Kaake
SpeciesList	scientific name: Human immunodeficiency virus; NCBI TaxID: 12721; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-14 04:27:34	ID requested
⏵ 1	2021-11-03 03:00:11	announced

Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ, Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics, 20():100132(2021) [pubmed]

submitter keyword: XL-MS, DSSO, HIV Vif, APOBEC3G, integrative modeling

Nevan J. Krogan
contact affiliation	QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA J. David Gladstone Institutes, San Francisco, CA, USA Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
contact email	nevan.krogan@ucsf.edu
lab head
Robyn Kaake
contact affiliation	Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
contact email	robyn.kaake@gladstone.ucsf.edu
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/2021/11/PXD025391

PRIDE project URI

• PRIDE
  1. PXD025391
     1. Label: PRIDE project
     2. Name: A3G-Vif-CBFB-CRL5 Cross-Linking with DSSO