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- PDB-9eg8: Cryo-EM structure of COP9 signalosome precatalytic state with ned... -

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Basic information

Entry
Database: PDB / ID: 9eg8
TitleCryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A
Components
  • (COP9 signalosome complex subunit ...) x 8
  • Cullin-4A
  • E3 ubiquitin-protein ligase RBX1
  • NEDD8
KeywordsSIGNALING PROTEIN / COP9 / COP9 signalosome / signalosome / deneddylation / CSN5 / metalloprotease / N8CUL4A / CUL4A / deneddylation complex
Function / homology
Function and homology information


COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / negative regulation of granulocyte differentiation / exosomal secretion / GTPase inhibitor activity / 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 / negative regulation of granulocyte differentiation / 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 / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / COP9 signalosome / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cellular response to chemical stress / regulation of DNA damage checkpoint / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / regulation of nucleotide-excision repair / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / regulation of JNK cascade / Hydrolases; Acting on peptide bonds (peptidases) / metal-dependent deubiquitinase activity / RHOBTB1 GTPase cycle / negative regulation of response to oxidative stress / VCB complex / 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 / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / TGF-beta receptor signaling activates SMADs / hemopoiesis / response to light stimulus / regulation of proteolysis / cullin family protein binding / skeletal muscle cell differentiation / regulation of postsynapse assembly / somatic stem cell population maintenance / anatomical structure morphogenesis / protein monoubiquitination / positive regulation of G1/S transition of mitotic cell cycle / : / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / JNK cascade / transcription-coupled nucleotide-excision repair / translation initiation factor activity / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / negative regulation of insulin receptor signaling pathway / intrinsic apoptotic signaling pathway / post-translational protein modification / T cell activation / Regulation of BACH1 activity / cellular response to amino acid stimulus / Degradation of DVL / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / G1/S transition of mitotic cell cycle / Recognition of DNA damage by PCNA-containing replication complex / negative regulation of canonical Wnt signaling pathway / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / 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 / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / protein modification process / DNA Damage Recognition in GG-NER / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / modification-dependent protein catabolic process / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / protein tag activity
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 / PCI/PINT associated module / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / 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 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-4A / Ubiquitin-like protein NEDD8 / COP9 signalosome complex subunit 6 / 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: 3.39 Å
AuthorsShi, H. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A
Authors: Shi, H. / Zheng, N.
History
DepositionNov 21, 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
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: COP9 signalosome complex subunit 5
I: NEDD8
J: Cullin-4A
A: COP9 signalosome complex subunit 1
B: COP9 signalosome complex subunit 2
C: COP9 signalosome complex subunit 3
D: COP9 signalosome complex subunit 4
F: COP9 signalosome complex subunit 6
G: COP9 signalosome complex subunit 7b
H: COP9 signalosome complex subunit 8
K: E3 ubiquitin-protein ligase RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,57314
Polymers437,37711
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 EABCDFGH

#1: 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 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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

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Protein , 3 types, 3 molecules IJK

#2: 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
#3: Protein Cullin-4A / CUL-4A


Mass: 87814.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Escherichia coli (E. coli) / References: UniProt: Q13619
#11: 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: Escherichia coli (E. coli)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase

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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 COP9 signalosome deneddylation complex with cullin1
Type: COMPLEX / Entity ID: #4-#7, #1, #8-#10, #2-#3, #11 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
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
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163795 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4D10

4d10


Accession code: 4D10 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325185
ELECTRON MICROSCOPYf_angle_d0.60933968
ELECTRON MICROSCOPYf_dihedral_angle_d4.6063337
ELECTRON MICROSCOPYf_chiral_restr0.043818
ELECTRON MICROSCOPYf_plane_restr0.0044342

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