Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes

被引：5

作者：

Kaake, Robyn M. ^{[1
,2
,3
]}

Echeverria, Ignacia ^{[1
,4
]}

Kim, Seung Joong ^{[4
,10
,11
]}

Von Dollen, John ^{[1
,2
]}

Chesarino, Nicholas M. ^{[5
,6
]}

Feng, Yuqing ^{[7
,12
]}

Yu, Clinton ^{[8
]}

Ta, Hai ^{[9
]}

Chelico, Linda ^{[7
]}

Huang, Lan ^{[8
]}

Gross, John ^{[2
,9
]}

Sali, Andrej ^{[2
,4
,9
]}

Krogan, Nevan J. ^{[1
,2
,3
]}

机构：

[1] Univ Calif San Francisco, Dept Cellular & Mol Pharmacol, Calif Inst Quantitat Biosci, San Francisco, CA 94143 USA

[2] Univ Calif San Francisco, Quantitat Biosci Inst, San Francisco, CA 94143 USA

[3] J David Gladstone Inst, Gladstone Inst Data Sci & Biotechnol, San Francisco, CA 94158 USA

[4] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA

[5] Fred Hutchinson Canc Res Ctr, Div Human Biol, 1124 Columbia St, Seattle, WA 98104 USA

[6] Fred Hutchinson Canc Res Ctr, Div Basic Sci, 1124 Columbia St, Seattle, WA 98104 USA

[7] Univ Saskatchewan, Dept Biochem, Immunol, Microbiol, Saskatoon, SK, Canada

[8] Univ Calif Irvine, Dept Physiol & Biophys, Irvine, CA 92717 USA

[9] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 USA

[10] Korea Adv Inst Sci & Technol KAIST, Dept Phys, Daejeon 34141, South Korea

[11] Korea Adv Inst Sci & Technol KAIST, Dept Biol Sci, Daejeon 34141, South Korea

[12] Univ Toronto, Dept Immunol, 1 Kings Coll Cir MSB 7302, Toronto, ON M5S 1A8, Canada

来源：

MOLECULAR & CELLULAR PROTEOMICS | 2021年 / 20卷

基金：

加拿大健康研究院; 美国国家卫生研究院; 新加坡国家研究基金会;

关键词：

HUMAN-IMMUNODEFICIENCY-VIRUS; SINGLE AMINO-ACID; APOBEC3G CATALYTIC DOMAIN; UBIQUITIN LIGASE COMPLEX; VIRAL INFECTIVITY FACTOR; HIV-1; VIF; TYPE-1; CBF-BETA; MOLECULAR ARCHITECTURE; CRYSTAL-STRUCTURE;

D O I：

10.1016/j.mcpro.2021.100132

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 (CBF beta) to determine the structure of the (A3G-Vif-CRL5-CBF beta) 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-CBF beta 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.

引用

页数：18