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- PDB-9qo3: Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex -

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Basic information

Entry
Database: PDB / ID: 9qo3
TitleDissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
Components
  • (COP9 signalosome complex subunit ...) x 9
  • (S-phase kinase-associated protein ...) x 2
  • Cullin-1
  • Cyclin-dependent kinases regulatory subunit 1
KeywordsLIGASE / COP9 signalosome / Cullin-RING E3 LIGASE
Function / homology
Function and homology information


negative regulation of protein localization to nucleolus / negative regulation of protein neddylation / COP9 signalosome assembly / macrophage migration inhibitory factor binding / regulation of xenophagy / regulation of IRE1-mediated unfolded protein response / Parkin-FBXW7-Cul1 ubiquitin ligase complex / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity ...negative regulation of protein localization to nucleolus / negative regulation of protein neddylation / COP9 signalosome assembly / macrophage migration inhibitory factor binding / regulation of xenophagy / regulation of IRE1-mediated unfolded protein response / Parkin-FBXW7-Cul1 ubiquitin ligase complex / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / F-box domain binding / synaptic assembly at neuromuscular junction / Aberrant regulation of mitotic exit in cancer due to RB1 defects / activation of NF-kappaB-inducing kinase activity / protein deneddylation / regulation of cell cycle process / neural crest cell differentiation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / regulation of BMP signaling pathway / PcG protein complex / regulation of mitophagy / COP9 signalosome / deubiquitinase activity / regulation of centrosome duplication / cullin-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cyclin-dependent protein serine/threonine kinase activator activity / regulation of TOR signaling / protein neddylation / ubiquitin ligase activator activity / regulation of DNA damage checkpoint / Hydrolases; Acting on peptide bonds (peptidases) / regulation of JNK cascade / regulation of DNA damage response, signal transduction by p53 class mediator / RHOBTB1 GTPase cycle / metal-dependent deubiquitinase activity / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / intercellular bridge / Prolactin receptor signaling / limb development / ubiquitin ligase complex scaffold activity / centrosome duplication / response to light stimulus / cilium assembly / JNK cascade / protein monoubiquitination / cullin family protein binding / protein K63-linked ubiquitination / cyclin-dependent protein kinase holoenzyme complex / positive regulation of double-strand break repair via homologous recombination / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / translation initiation factor activity / animal organ morphogenesis / intrinsic apoptotic signaling pathway / post-translational protein modification / regulation of mitotic cell cycle / molecular function activator activity / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / ubiquitin binding / G1/S transition of mitotic cell cycle / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / cell population proliferation / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / regulation of circadian rhythm / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / beta-catenin binding / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / NOTCH1 Intracellular Domain Regulates Transcription / Degradation of beta-catenin by the destruction complex / DNA Damage Recognition in GG-NER / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / neuron differentiation / Formation of TC-NER Pre-Incision Complex / metallopeptidase activity / protein polyubiquitination / Interleukin-1 signaling / cellular response to UV
Similarity search - Function
COP9 signalosome complex, subunit 9, metazoa / Myeloma-overexpressed-like / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / COP9 signalosome complex subunit 7, helix I / : ...COP9 signalosome complex, subunit 9, metazoa / Myeloma-overexpressed-like / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 4, helix turn helix domain / : / CSN4/RPN5/eIF3a helix turn helix domain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / : / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 2, C-terminal helix / Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / PCI/PINT associated module / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / : / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Cyclin-dependent kinases regulatory subunit 1 / COP9 signalosome complex subunit 2 / S-phase kinase-associated protein 1 / COP9 signalosome complex subunit 1 / S-phase kinase-associated protein 2 / Cullin-1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 9 / COP9 signalosome complex subunit 5 ...INOSITOL HEXAKISPHOSPHATE / Cyclin-dependent kinases regulatory subunit 1 / COP9 signalosome complex subunit 2 / S-phase kinase-associated protein 1 / COP9 signalosome complex subunit 1 / S-phase kinase-associated protein 2 / Cullin-1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 9 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7b / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsDing, S. / Clapperton, J.A. / Maeots, M.E. / Enchev, R.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2059 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of CSN-mediated SCF deneddylation.
Authors: Shan Ding / Julie A Clapperton / Märt-Erik Mäeots / Simone Kunzelmann / Mohammed Shaaban / Radoslav I Enchev /
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 ...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.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 1
C: COP9 signalosome complex subunit 3
D: COP9 signalosome complex subunit 4
E: COP9 signalosome complex subunit 5
F: COP9 signalosome complex subunit 6
G: COP9 signalosome complex subunit 7b
H: COP9 signalosome complex subunit 8
I: Cullin-1
L: S-phase kinase-associated protein 1
M: S-phase kinase-associated protein 2
N: Cyclin-dependent kinases regulatory subunit 1
B: COP9 signalosome complex subunit 2
P: COP9 signalosome complex subunit 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)501,16215
Polymers500,43613
Non-polymers7252
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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COP9 signalosome complex subunit ... , 9 types, 9 molecules ACDEFGHBP

#1: Protein COP9 signalosome complex subunit 1 / Signalosome subunit 1 / G protein pathway suppressor 1 / GPS-1 / JAB1-containing signalosome ...Signalosome subunit 1 / G protein pathway suppressor 1 / GPS-1 / JAB1-containing signalosome subunit 1 / Protein MFH


Mass: 55606.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPS1, COPS1, CSN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13098
#2: Protein COP9 signalosome complex subunit 3 / SGN3 / Signalosome subunit 3 / JAB1-containing signalosome subunit 3


Mass: 47924.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS3, CSN3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UNS2
#3: Protein COP9 signalosome complex subunit 4 / SGN4 / Signalosome subunit 4 / JAB1-containing signalosome subunit 4


Mass: 46322.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS4, CSN4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BT78
#4: Protein COP9 signalosome complex subunit 5 / SGN5 / Signalosome subunit 5 / Jun activation domain-binding protein 1


Mass: 37621.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS5, CSN5, JAB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases)
#5: Protein COP9 signalosome complex subunit 6 / Signalosome subunit 6 / JAB1-containing signalosome subunit 6 / MOV34 homolog / Vpr-interacting protein / hVIP


Mass: 36203.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS6, CSN6, HVIP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L5N1
#6: Protein COP9 signalosome complex subunit 7b / SGN7b / Signalosome subunit 7b / JAB1-containing signalosome subunit 7b


Mass: 29656.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS7B, CSN7B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H9Q2
#7: Protein COP9 signalosome complex subunit 8 / Signalosome subunit 8 / COP9 homolog / hCOP9 / JAB1-containing signalosome subunit 8


Mass: 23245.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS8, CSN8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99627
#12: Protein COP9 signalosome complex subunit 2 / Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor- ...Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor-interacting protein 15 / TRIP-15


Mass: 51664.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS2, CSN2, TRIP15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61201
#13: Protein COP9 signalosome complex subunit 9 / CSN acidic protein / CSNAP / Myeloma-overexpressed gene 2 protein


Mass: 6213.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS9, MYEOV2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WXC6

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Protein , 2 types, 2 molecules IN

#8: Protein Cullin-1 / CUL-1


Mass: 89800.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13616
#11: Protein Cyclin-dependent kinases regulatory subunit 1 / CKS-1


Mass: 9679.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61024

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S-phase kinase-associated protein ... , 2 types, 2 molecules LM

#9: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18679.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63208
#10: Protein S-phase kinase-associated protein 2 / Cyclin-A/CDK2-associated protein p45 / F-box protein Skp2 / F-box/LRR-repeat protein 1 / p45skp2


Mass: 47817.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13309

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Non-polymers , 3 types, 3 molecules

#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
19-subunit COP9 signalosome and SCFSkp2-Cks1 complexCOMPLEX#1-#130RECOMBINANT
29-subunit COP9 signalosomeCOMPLEX#1-#7, #131RECOMBINANTE104A
3SCFCOMPLEX#8-#111RECOMBINANT
4Skp1-Skp2-Cks1COMPLEX#9-#113RECOMBINANT
5Cullin-1COMPLEX#83RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11
22
44
54NO
65
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
54Homo sapiens (human)9606
64Homo sapiens (human)9606
75Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
54Spodoptera frugiperda (fall armyworm)7108
64Escherichia coli BL21(DE3) (bacteria)469008
75Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5 / Details: 15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.21.1_5286model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54098 / Symmetry type: POINT
RefinementHighest resolution: 4.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00329357
ELECTRON MICROSCOPYf_angle_d0.63439732
ELECTRON MICROSCOPYf_dihedral_angle_d4.7123931
ELECTRON MICROSCOPYf_chiral_restr0.0394556
ELECTRON MICROSCOPYf_plane_restr0.0055074

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