Cullin–RING ubiquitin E3 ligase regulation by the COP9 signalosome

Cavadini, Simone; Fischer, Eric S.; Bunker, Richard D.; Potenza, Alessandro; Lingaraju, Gondichatnahalli M.; Goldie, Kenneth N.; Mohamed, Weaam I.; Faty, Mahamadou; Petzold, Georg; Beckwith, Rohan E. J.; Tichkule, Ritesh B.; Hassiepen, Ulrich; Abdulrahman, Wassim; Pantelic, Radosav S.; Matsumoto, Syota; Sugasawa, Kaoru; Stahlberg, Henning; Thomä, Nicolas H.

doi:10.1038/nature17416

Cited by 214Ubiquitin and proteasome pathwaysProtein Degradation and InhibitorsEnzyme Structure and Function

Cullin–RING ubiquitin E3 ligase regulation by the COP9 signalosome

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Cavadini, Simone, Fischer, Eric S., Bunker, Richard D., Potenza, Alessandro, Lingaraju, Gondichatnahalli M., Goldie, Kenneth N., Mohamed, Weaam I., Faty, Mahamadou +10 more·2016·Nature

DOI 10.1038/nature17416

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Abstract

The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A-RBX1-DDB1-DDB2 complex (CRL4A(DDB2)) monitors the genome for ultraviolet-light-induced DNA damage. CRL4A(DBB2) is inactive in the absence of damaged DNA and requires CSN to regulate the repair process. The structural basis of CSN binding to CRL4A(DDB2) and the principles of CSN activation are poorly understood. Here we present cryo-electron microscopy structures for CSN in complex with neddylated CRL4A ligases to 6.4 Å resolution. The CSN conformers defined by cryo-electron microscopy and a novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by neddylated CRLs. We find that CSN and a substrate cannot bind simultaneously to CRL4A, favouring a deneddylated, inactive state for substrate-free CRL4 complexes. These architectural and regulatory principles appear conserved across CRL families, allowing global regulation by CSN.

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The conformational dynamics of unneddylated CRLs would enable transitioning between the different conformations coordinating cycles of neddylation/deneddylation with CAND1-driven substrate-receptor exchange.
“it seems likely that the conformational dynamics of unneddylated CRLs (Extended Data Figure 2) would enable transitioning between the different conformations coordinating cycles of neddylation/deneddylation with CAND1-driven substrate-receptor exchange39,46–49.”
From NEDD8 nucleates a multivalent cullin–RING–UBE2D ubiquitin ligation assembly (2020) · cites this paper as [48]

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Authors: Cavadini, S., Fischer, E. S., Bunker, R. D., Potenza, A., Lingaraju, G. M., Goldie, K. N., Mohamed, W. I., Faty, M., Petzold, G., Beckwith, R. E. J., Tichkule, R. B., Hassiepen, U., Abdulrahman, W., Pantelic, R. S., Matsumoto, S., Sugasawa, K., Stahlberg, H., & Thomä, N. H.
Affiliations: University of Basel (CH)
Harvard University (US)
Novartis (Switzerland) (CH)
Biosignal Research Center, Kobe University (JP)
Corresponding author: Thomä, Nicolas H.
ORCID: Cavadini, Simone
Fischer, Eric S.
Bunker, Richard D.
Goldie, Kenneth N.
Mohamed, Weaam I.
Petzold, Georg
Beckwith, Rohan E. J.
Abdulrahman, Wassim
Matsumoto, Syota
Sugasawa, Kaoru
Stahlberg, Henning
Thomä, Nicolas H.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-03-30
Volume: 531
Issue: 7596
Pages: 598-603
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature17416
OpenAlex: W2327577222
Cited by: 213
References: 49
Citations by year: 2026: 15 · 2025: 14 · 2024: 16 · 2023: 18 · 2022: 13 · 2021: 25 · 2020: 45 · 2019: 23 · 2018: 14 · 2017: 21 · 2016: 8 · 2013: 1
FWCI: 11.43
Type: journal article
Language: en
Open access: green
infoscience.epfl.ch
Licence: cc-by-nc-nd
www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
DORA PSI (Paul Scherrer Institute) (submittedVersion)
edoc (University of Basel) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
Funders: Japan Society for the Promotion of Science
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords: COP9 signalosome, NEDD8, induced fit, UV-induced DNA damage, DNA repair, protein degradation, substrate binding
MeSH terms: COP9 Signalosome Complex, Allosteric Regulation, Apoproteins, Binding Sites, Carrier Proteins, DNA Damage, DNA-Binding Proteins, Humans, Kinetics, Models, Molecular, Peptide Hydrolases, Protein Binding, Ubiquitins, Crystallography, X-Ray, Cryoelectron Microscopy, Cullin Proteins, Multiprotein Complexes, Ubiquitination, Biocatalysis

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Cullin–RING ubiquitin E3 ligase regulation by the COP9 signalosome

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