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- PDB-9qo1: Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP... -

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Basic information

Entry
Database: PDB / ID: 9qo1
TitleActivated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure
Components
  • (COP9 signalosome complex subunit ...) x 9
  • Cullin-1
  • E3 ubiquitin-protein ligase RBX1
  • NEDD8
KeywordsLIGASE / Cullin-RING E3 ligases / COP9 signalosome
Function / homology
Function and homology information


negative regulation of protein neddylation / negative regulation of protein localization to nucleolus / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / Parkin-FBXW7-Cul1 ubiquitin ligase complex / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity ...negative regulation of protein neddylation / negative regulation of protein localization to nucleolus / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / Parkin-FBXW7-Cul1 ubiquitin ligase complex / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / activation of NF-kappaB-inducing kinase activity / eukaryotic translation initiation factor 3 complex / negative regulation of beige fat cell differentiation / cellular response to camptothecin / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / COP9 signalosome / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / Hydrolases; Acting on peptide bonds (peptidases) / protein K27-linked ubiquitination / regulation of JNK cascade / metal-dependent deubiquitinase activity / negative regulation of response to oxidative stress / RHOBTB1 GTPase cycle / regulation of DNA damage response, signal transduction by p53 class mediator / VCB complex / inner cell mass cell proliferation / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / negative regulation of mitophagy / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / skeletal muscle cell differentiation / : / regulation of postsynapse assembly / cullin family protein binding / response to light stimulus / anatomical structure morphogenesis / protein monoubiquitination / site of DNA damage / JNK cascade / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / protein K48-linked ubiquitination / negative regulation of insulin receptor signaling pathway / translation initiation factor activity / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / post-translational protein modification / animal organ morphogenesis / T cell activation / Regulation of BACH1 activity / protein modification process / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of canonical NF-kappaB signal transduction / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / cellular response to amino acid stimulus / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / G1/S transition of mitotic cell cycle / Degradation of GLI1 by the proteasome / Iron uptake and transport / negative regulation of canonical Wnt signaling pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Recognition of DNA damage by PCNA-containing replication complex / Hedgehog 'on' state / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / DNA Damage Recognition in GG-NER
Similarity search - Function
COP9 signalosome complex, subunit 9, metazoa / Myeloma-overexpressed-like / 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 / : ...COP9 signalosome complex, subunit 9, metazoa / Myeloma-overexpressed-like / 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 / Nedd8-like ubiquitin / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin, N-terminal / Cullin protein neddylation domain / : / : / Cullin, conserved site / : / : / Cullin alpha solenoid domain / PSMD12/CSN4, N-terminal / Cullin family signature. / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / 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 / 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. / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Tetratricopeptide-like helical domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-1 / Ubiquitin-like protein NEDD8 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 9 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 ...INOSITOL HEXAKISPHOSPHATE / COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-1 / Ubiquitin-like protein NEDD8 / 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: 3.23 Å
AuthorsDing, S. / Clapperton, J.A. / Maeots, M.E. / Shaaban, M. / 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 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 1
B: COP9 signalosome complex subunit 2
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
J: E3 ubiquitin-protein ligase RBX1
P: COP9 signalosome complex subunit 9
K: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,91316
Polymers445,05612
Non-polymers8564
Water00
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 ABCDEFGHP

#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 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
#3: 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
#4: Protein COP9 signalosome complex subunit 4 / 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
#5: Protein COP9 signalosome complex subunit 5 / SGN5 / Signalosome subunit 5 / Jun activation domain-binding protein 1


Mass: 37554.672 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)
#6: 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
#7: 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
#8: 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
#11: 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 , 3 types, 3 molecules IJK

#9: 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
#10: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
#12: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8573.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15843

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Non-polymers , 2 types, 4 molecules

#13: 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
#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationN

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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-IDSource
1COP9 signalosome and neddylated SCF complexCOMPLEX#2-#12, #10RECOMBINANT
2COP9 signalosomeCOMPLEX#2-#8, #11, #11RECOMBINANT
3Neddylated Cullin-1/Rbx1 complexCOMPLEX#9-#101RECOMBINANT
4Cullin-1/Rbx1COMPLEX#9-#103RECOMBINANT
5Nedd8COMPLEX#123RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
44
55
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
65Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Spodoptera frugiperda (fall armyworm)7108
54Spodoptera frugiperda (fall armyworm)7108
65Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
SpecimenEmbedding 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
9PHENIX1.21_5207model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 556830 / Symmetry type: POINT
RefinementHighest resolution: 3.23 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325838
ELECTRON MICROSCOPYf_angle_d0.56134889
ELECTRON MICROSCOPYf_dihedral_angle_d6.683509
ELECTRON MICROSCOPYf_chiral_restr0.0363940
ELECTRON MICROSCOPYf_plane_restr0.0044449

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