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- PDB-9eg1: COP9 signalosome deneddylation complex with cullin-5 -

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Basic information

Entry
Database: PDB / ID: 9eg1
TitleCOP9 signalosome deneddylation complex with cullin-5
Components
  • (COP9 signalosome complex subunit ...) x 8
  • Cullin-5
  • NEDD8
  • RING-box protein 2
KeywordsSIGNALING PROTEIN / COP9 / COP9 signalosome / signalosome / NEDD8 / N8CUL5 / deneddylation / CSN5 / CUL5 / metalloprotease
Function / homology
Function and homology information


COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / ERBB2 signaling pathway / deNEDDylase activity / protein deneddylation / regulation of protein neddylation ...COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / ERBB2 signaling pathway / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / activation of NF-kappaB-inducing kinase activity / eukaryotic translation initiation factor 3 complex / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / COP9 signalosome / regulation of neuron migration / protein K11-linked ubiquitination / protein neddylation / NEDD8 ligase activity / Hydrolases; Acting on peptide bonds (peptidases) / RHOBTB1 GTPase cycle / metal-dependent deubiquitinase activity / response to redox state / regulation of JNK cascade / regulation of DNA damage response, signal transduction by p53 class mediator / Cul5-RING ubiquitin ligase complex / inner cell mass cell proliferation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / response to light stimulus / cullin family protein binding / skeletal muscle cell differentiation / regulation of postsynapse assembly / anatomical structure morphogenesis / site of DNA damage / : / endoplasmic reticulum unfolded protein response / JNK cascade / translation initiation factor activity / intrinsic apoptotic signaling pathway / post-translational protein modification / protein modification process / G1/S transition of mitotic cell cycle / Iron uptake and transport / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / modification-dependent protein catabolic process / DNA Damage Recognition in GG-NER / Evasion by RSV of host interferon responses / Downregulation of ERBB2 signaling / calcium channel activity / Formation of TC-NER Pre-Incision Complex / protein tag activity / metallopeptidase activity / neuron differentiation / synaptic vesicle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell junction / intracellular protein localization / UCH proteinases / transcription corepressor activity / Cargo recognition for clathrin-mediated endocytosis / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / in utero embryonic development / transcription by RNA polymerase II / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / protein phosphorylation / regulation of cell cycle / postsynapse / nuclear speck / protein ubiquitination / translation / copper ion binding / negative regulation of cell population proliferation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding
Similarity search - Function
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 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 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 protein neddylation domain / : / : / : / : / 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, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin alpha solenoid domain / PCI/PINT associated module / Cullin / 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 / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / 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
COP9 signalosome complex subunit 2 / COP9 signalosome complex subunit 1 / Ubiquitin-like protein NEDD8 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / Cullin-5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7b / RING-box protein 2 / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsShi, H. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2026
Title: CSN5i-3 is an orthosteric molecular glue inhibitor of COP9 signalosome.
Authors: Huigang Shi / Xiaorong Wang / Clinton Yu / Haibin Mao / Fenglong Jiao / Merav Braitbard / Ben Shor / Zhongsheng Zhang / Thomas R Hinds / Shiyun Cao / Erkang Fan / Dina Schneidman-Duhovny / ...Authors: Huigang Shi / Xiaorong Wang / Clinton Yu / Haibin Mao / Fenglong Jiao / Merav Braitbard / Ben Shor / Zhongsheng Zhang / Thomas R Hinds / Shiyun Cao / Erkang Fan / Dina Schneidman-Duhovny / Lan Huang / Ning Zheng /
Abstract: Orthosteric inhibitors block enzyme active sites and prevent substrates from binding. Enhancing their specificity through substrate dependence seems inherently unlikely, as their mechanism hinges on ...Orthosteric inhibitors block enzyme active sites and prevent substrates from binding. Enhancing their specificity through substrate dependence seems inherently unlikely, as their mechanism hinges on direct competition rather than selective recognition. Here we show that a molecular glue mechanism unexpectedly imparts substrate-dependent potency to CSN5i-3, an orthosteric inhibitor of the COP9 signalosome (CSN). We first confirm that CSN5i-3 inhibits CSN, which catalyses NEDD8 (N8) deconjugation from the cullin-RING ubiquitin ligases, by occupying the active site of its catalytic subunit, CSN5, and directly competing with the iso-peptide bond substrate. Notably, the orthosteric inhibitor binds free CSN with only micromolar affinity, yet achieves nanomolar potency in blocking its deneddylase activity. Cryogenic electron microscopy structures of the enzyme-substrate-inhibitor complex reveal that active site-engaged CSN5i-3 occludes the substrate iso-peptide linkage while simultaneously extending an N8-binding exosite of CSN5, acting as a molecular glue to cement the N8-CSN5 interaction. The cooperativity of this trimolecular CSN5i-3-N8-CSN5 assembly, in turn, sequesters CSN5i-3 at its binding site, conferring high potency to the orthosteric inhibitor despite its low affinity for the free enzyme. Together, our findings highlight the modest affinity requirements of molecule glues for individual target proteins and establish orthosteric molecular glue inhibitors as a new class of substrate-dependent enzyme antagonists.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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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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Revision 1.2Feb 25, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.2Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: COP9 signalosome complex subunit 2
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
J: Cullin-5
K: RING-box protein 2
A: COP9 signalosome complex subunit 1
C: COP9 signalosome complex subunit 3
I: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,25214
Polymers441,05611
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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COP9 signalosome complex subunit ... , 8 types, 8 molecules BDEFGHAC

#1: Protein COP9 signalosome complex subunit 2 / SGN2 / Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid ...SGN2 / Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor-interacting protein 15 / TR-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: Escherichia coli (E. coli) / References: UniProt: P61201
#2: 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: Escherichia coli (E. coli) / References: UniProt: Q9BT78
#3: Protein COP9 signalosome complex subunit 5 / SGN5 / Signalosome subunit 5 / Jun activation domain-binding protein 1


Mass: 37562.719 Da / Num. of mol.: 1 / Mutation: E76A, D151N
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)
#4: Protein COP9 signalosome complex subunit 6 / SGN6 / Signalosome subunit 6 / JAB1-containing signalosome subunit 6 / MOV34 homolog / Vpr- ...SGN6 / 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: Escherichia coli (E. coli) / References: UniProt: Q7L5N1
#5: 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: Escherichia coli (E. coli) / References: UniProt: Q9H9Q2
#6: Protein COP9 signalosome complex subunit 8 / SGN8 / 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: Escherichia coli (E. coli) / References: UniProt: Q99627
#9: Protein COP9 signalosome complex subunit 1 / SGN1 / Signalosome subunit 1 / G protein pathway suppressor 1 / GPS-1 / JAB1-containing signalosome ...SGN1 / 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: Escherichia coli (E. coli) / References: UniProt: Q13098
#10: 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: Escherichia coli (E. coli) / References: UniProt: Q9UNS2

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Protein , 3 types, 3 molecules JKI

#7: Protein Cullin-5 / CUL-5 / Vasopressin-activated calcium-mobilizing receptor 1 / VACM-1


Mass: 91085.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93034
#8: Protein RING-box protein 2 / Rbx2 / CKII beta-binding protein 1 / CKBBP1 / RING finger protein 7 / Regulator of cullins 2 / ...Rbx2 / CKII beta-binding protein 1 / CKBBP1 / RING finger protein 7 / Regulator of cullins 2 / Sensitive to apoptosis gene protein


Mass: 12697.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF7, RBX2, ROC2, SAG / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBF6, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
#11: 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: 9086.562 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 (E. coli) / References: UniProt: Q15843

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Non-polymers , 1 types, 3 molecules

#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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

ComponentName: The complex of human COP9 signalosome with NEDD8 and CSN5i-3
Type: COMPLEX / Entity ID: #9, #1, #10, #2-#6, #11, #7-#8 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239911 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 4D10

4d10


Accession code: 4D10 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324141
ELECTRON MICROSCOPYf_angle_d0.73232653
ELECTRON MICROSCOPYf_dihedral_angle_d4.3513292
ELECTRON MICROSCOPYf_chiral_restr0.0413749
ELECTRON MICROSCOPYf_plane_restr0.0044200

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