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Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4088-4098. doi: 10.1073/pnas.1915542117. Epub 2020 Feb 7.

Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.

Author information

1
Department of Physiology & Biophysics, University of California, Irvine, CA 92697.
2
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.
3
Department of Pharmacology, University of Washington, Seattle, WA 98195.
4
Department of Chemistry, University of California, Irvine, CA 92697.
5
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195.
6
Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158.
7
Department of Physiology & Biophysics, University of California, Irvine, CA 92697; lanhuang@uci.edu.

Abstract

The COP9 signalosome (CSN) is an evolutionarily conserved eight-subunit (CSN1-8) protein complex that controls protein ubiquitination by deneddylating Cullin-RING E3 ligases (CRLs). The activation and function of CSN hinges on its structural dynamics, which has been challenging to decipher by conventional tools. Here, we have developed a multichemistry cross-linking mass spectrometry approach enabled by three mass spectometry-cleavable cross-linkers to generate highly reliable cross-link data. We applied this approach with integrative structure modeling to determine the interaction and structural dynamics of CSN with the recently discovered ninth subunit, CSN9, in solution. Our results determined the localization of CSN9 binding sites and revealed CSN9-dependent structural changes of CSN. Together with biochemical analysis, we propose a structural model in which CSN9 binding triggers CSN to adopt a configuration that facilitates CSN-CRL interactions, thereby augmenting CSN deneddylase activity. Our integrative structure analysis workflow can be generalized to define in-solution architectures of dynamic protein complexes that remain inaccessible to other approaches.

KEYWORDS:

COP9 signalosome; architectures of protein complexes; cross-linking mass spectrometry; integrative structure modeling; structural dynamics

PMID:
32034103
PMCID:
PMC7049115
[Available on 2020-08-07]
DOI:
10.1073/pnas.1915542117

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