Evidence map›Paper›PMID 32034103›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2020

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

Craig Gutierrez, Ilan E Chemmama, Haibin Mao, Clinton Yu, Ignacia Echeverria, Sarah A Block, Scott D Rychnovsky, Ning Zheng, Andrej Sali, Lan Huang

Open access · greenAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.

0numbers the graph read from it
0cells of the map it votes in
45citing papers in PubMed
5.7field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

45 citing papers in PubMed, 87 citations in OpenAlex.

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  16. Review
  17. Fungal COP9 signalosome assembly requires connection of two trimeric intermediates for integration of intrinsic deneddylase.Proceedings of the National Academy of Sciences of the United States of America · 2023
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 5 institutions in 1 country.

Craig GutierrezDepartment of Physiology & Biophysics, University of California, Irvine, CA 92697.
Ilan E ChemmamaDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.
Haibin MaoDepartment of Pharmacology, University of Washington, Seattle, WA 98195.
Clinton YuDepartment of Physiology & Biophysics, University of California, Irvine, CA 92697.
Ignacia EcheverriaDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.
Sarah A BlockDepartment of Chemistry, University of California, Irvine, CA 92697.
Scott D RychnovskyDepartment of Chemistry, University of California, Irvine, CA 92697.
Ning ZhengDepartment of Pharmacology, University of Washington, Seattle, WA 98195.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.ORCID 0000-0003-0435-6197
Lan HuangDepartment of Physiology & Biophysics, University of California, Irvine, CA 92697; lanhuang@uci.edu.ORCID 0000-0002-3140-4687
University of California, Irvine · USUniversity of California, San Francisco · USHoward Hughes Medical Institute · USQB3 · USUniversity of Washington · US

Funding

TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
Proteomics of the Proteasome Interacting NetworksR01GM074830 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI HUANG, LAN · 2005 to 2022
$6.1M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Structural dynamics and function of the COP9 signalosomeR01GM130144 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI HUANG, LAN · 2018 to 2021
$1.2M
High Performance Computer for Computational BiosciencesS10OD021596 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2016 to 2016
$443k
Howard Hughes Medical InstituteNIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM074830NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM130144NIGMS NIH HHS T32 GM008284NIH HHS S10 OD021596
6 · The paper itself

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.

Indexed as

COP9 Signalosome ComplexCross-Linking ReagentsCrystallography, X-RayHumansMass SpectrometryModels, MolecularProtein ConformationCOP9 Signalosome ComplexCross-Linking Reagentsarchitectures of protein complexesCOP9 signalosomecross-linking mass spectrometryintegrative structure modelingstructural dynamics

Identifiers

PMID32034103
PMCPMC7049115
OpenAlexW3005394826

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.