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Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes
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 contac...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Biochemistry and Molecular Biology
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459920/ https://www.ncbi.nlm.nih.gov/pubmed/34389466 http://dx.doi.org/10.1016/j.mcpro.2021.100132 |
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author | Kaake, Robyn M. Echeverria, Ignacia Kim, Seung Joong Von Dollen, John Chesarino, Nicholas M. Feng, Yuqing Yu, Clinton Ta, Hai Chelico, Linda Huang, Lan Gross, John Sali, Andrej Krogan, Nevan J. |
author_facet | Kaake, Robyn M. Echeverria, Ignacia Kim, Seung Joong Von Dollen, John Chesarino, Nicholas M. Feng, Yuqing Yu, Clinton Ta, Hai Chelico, Linda Huang, Lan Gross, John Sali, Andrej Krogan, Nevan J. |
author_sort | Kaake, Robyn M. |
collection | PubMed |
description | 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 factor Core Binding Factor Beta (CBFβ) to determine the structure of the (A3G-Vif-CRL5-CBFβ) complex. Using the MS-cleavable DSSO cross-linker to obtain a set of 132 cross-links within this reconstituted complex along with the atomic structures of the subunits and mutagenesis data, we computed an integrative structure model of the heptameric A3G-Vif-CRL5-CBFβ complex. The structure, which was validated using a series of tests, reveals that A3G is bound to Vif mostly through its N-terminal domain. Moreover, the model ensemble quantifies the dynamic heterogeneity of the A3G C-terminal domain and Cul5 positions. Finally, the model was used to rationalize previous structural, mutagenesis and functional data not used for modeling, including information related to the A3G-bound and unbound structures as well as mapping functional mutations to the A3G-Vif interface. The experimental and computational approach described here is generally applicable to other challenging host–pathogen protein complexes. |
format | Online Article Text |
id | pubmed-8459920 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Society for Biochemistry and Molecular Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-84599202021-09-28 Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes Kaake, Robyn M. Echeverria, Ignacia Kim, Seung Joong Von Dollen, John Chesarino, Nicholas M. Feng, Yuqing Yu, Clinton Ta, Hai Chelico, Linda Huang, Lan Gross, John Sali, Andrej Krogan, Nevan J. Mol Cell Proteomics Research 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 factor Core Binding Factor Beta (CBFβ) to determine the structure of the (A3G-Vif-CRL5-CBFβ) complex. Using the MS-cleavable DSSO cross-linker to obtain a set of 132 cross-links within this reconstituted complex along with the atomic structures of the subunits and mutagenesis data, we computed an integrative structure model of the heptameric A3G-Vif-CRL5-CBFβ complex. The structure, which was validated using a series of tests, reveals that A3G is bound to Vif mostly through its N-terminal domain. Moreover, the model ensemble quantifies the dynamic heterogeneity of the A3G C-terminal domain and Cul5 positions. Finally, the model was used to rationalize previous structural, mutagenesis and functional data not used for modeling, including information related to the A3G-bound and unbound structures as well as mapping functional mutations to the A3G-Vif interface. The experimental and computational approach described here is generally applicable to other challenging host–pathogen protein complexes. American Society for Biochemistry and Molecular Biology 2021-08-11 /pmc/articles/PMC8459920/ /pubmed/34389466 http://dx.doi.org/10.1016/j.mcpro.2021.100132 Text en © 2021 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Research Kaake, Robyn M. Echeverria, Ignacia Kim, Seung Joong Von Dollen, John Chesarino, Nicholas M. Feng, Yuqing Yu, Clinton Ta, Hai Chelico, Linda Huang, Lan Gross, John Sali, Andrej Krogan, Nevan J. Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes |
title | Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes |
title_full | Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes |
title_fullStr | Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes |
title_full_unstemmed | Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes |
title_short | Characterization of an A3G-Vif(HIV-1)-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes |
title_sort | characterization of an a3g-vif(hiv-1)-crl5-cbfβ structure using a cross-linking mass spectrometry pipeline for integrative modeling of host–pathogen complexes |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459920/ https://www.ncbi.nlm.nih.gov/pubmed/34389466 http://dx.doi.org/10.1016/j.mcpro.2021.100132 |
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