9QO3

Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex

Summary for 9QO3

• Entry DOI: 10.2210/pdb9qo3/pdb
• EMDB information: 53255
• Descriptor: COP9 signalosome complex subunit 1, S-phase kinase-associated protein 2, Cyclin-dependent kinases regulatory subunit 1, ... (16 entities in total)
• Functional Keywords: cop9 signalosome, cullin-ring e3 ligase, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 13
• Total formula weight: 501161.83

Authors

Ding, S.,Clapperton, J.A.,Maeots, M.E.,Enchev, R.I. (deposition date: 2025-03-25, release date: 2026-02-18)

Primary citation

Ding, S.,Clapperton, J.A.,Maeots, M.E.,Kunzelmann, S.,Shaaban, M.,Enchev, R.I.
Structural basis of CSN-mediated SCF deneddylation.
Nat Commun, 17:951-951, 2026

PubMed Abstract: Cullin-RING ligases (CRLs) are the largest family of E3 ligases, with ubiquitination activity dynamically regulated by neddylation and deneddylation by the COP9 signalosome (CSN). CSN-mediated deneddylation not only deactivates CRLs but also enables substrate receptor exchange. Although CSN is a promising drug target, the structural basis underlying its catalytic mechanism remains unclear. Here, we use cryo-electron microscopy (cryo-EM) to uncover distinct functional states of CSN-CRL (SCF) complexes, capturing key intermediates of the deneddylation cycle. We visualise an autoinhibited docking state and a catalytic intermediate in which CSN5 Ins-1 loop, RBX1 RING and neddylated Cullin WHB domains are repositioned for isopeptide cleavage. We further resolve four dissociation intermediates that define the stepwise release of CSN from its product, with RBX1 RING stabilising key interactions. Additionally, our structures locate CSNAP within a CSN3-CSN8 groove. Together, our study provides a mechanistic model for CSN function and informs the rational design of CSN-targeted therapeutics.

PubMed: 41577659
DOI: 10.1038/s41467-025-67566-y

Experimental method

ELECTRON MICROSCOPY (4.6 Å)