Dataset Information

A3G-Vif-CBFB-CRL5 Cross-Linking with DSSO

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human) Human Immunodeficiency Virus

SUBMITTER: Robyn Kaake

LAB HEAD: Nevan J. Krogan

PROVIDER: PXD025391 | Pride | 2021-11-03

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	Metadata_table_S1.txt	Txt
	PA.SwissProt.PN.RMK.A3GVifCRL5.fasta.random.concat	Fasta
	PN.RMK_LAIVif_HisCBFB.fasta	Fasta
	QE20150425-03.raw	Raw
	QE20150425-03_MS2.mgf	Mgf

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Publications

Characterization of an A3G-Vif<sub>HIV-1</sub>-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.

Kaake Robyn M RM Echeverria Ignacia I Kim Seung Joong SJ Von Dollen John J Chesarino Nicholas M NM Feng Yuqing Y Yu Clinton C Ta Hai H Chelico Linda L Huang Lan L Gross John J Sali Andrej A Krogan Nevan J NJ

Molecular & cellular proteomics : MCP 20210811

Structural analysis of host-pathogen protein complexes remains challenging, largely due to their structural heterogeneity. Here, we describe a pipeline for the structural characterization of these complexes using integrative structure modeling based on chemical cross-links and residue-protein contacts inferred from mutagenesis studies. We used this approach on the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription fact ...[more]

PMID: 34389466

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