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- EMDB-47983: COP9 signalosome deneddylation complex with cullin-5 -

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Basic information

Entry
Database: EMDB / ID: EMD-47983
TitleCOP9 signalosome deneddylation complex with cullin-5
Map data
Sample
  • Complex: The complex of human COP9 signalosome with NEDD8 and CSN5i-3
    • Protein or peptide: x 11 types
  • Ligand: x 1 types
KeywordsCOP9 / COP9 signalosome / signalosome / NEDD8 / N8CUL5 / deneddylation / CSN5 / CUL5 / metalloprotease / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsShi H / Zheng N
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47983.png

Downloads & links

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Map

FileDownload / File: emd_47983.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 334. Å		0.84 Å/pix.
x 400 pix.
= 334. Å		0.84 Å/pix.
x 400 pix.
= 334. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.35134062 - 0.93547153
Average (Standard dev.)0.005250017 (±0.018501956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 334.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The complex of human COP9 signalosome with NEDD8 and CSN5i-3

EntireName: The complex of human COP9 signalosome with NEDD8 and CSN5i-3
Components
  • Complex: The complex of human COP9 signalosome with NEDD8 and CSN5i-3
    • Protein or peptide: COP9 signalosome complex subunit 1
    • Protein or peptide: COP9 signalosome complex subunit 2
    • Protein or peptide: COP9 signalosome complex subunit 3
    • Protein or peptide: COP9 signalosome complex subunit 4
    • Protein or peptide: COP9 signalosome complex subunit 5
    • Protein or peptide: COP9 signalosome complex subunit 6
    • Protein or peptide: COP9 signalosome complex subunit 7b
    • Protein or peptide: COP9 signalosome complex subunit 8
    • Protein or peptide: NEDD8
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
  • Ligand: ZINC ION

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Supramolecule #1: The complex of human COP9 signalosome with NEDD8 and CSN5i-3

SupramoleculeName: The complex of human COP9 signalosome with NEDD8 and CSN5i-3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #9, #1, #10, #2-#6, #11, #7-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: COP9 signalosome complex subunit 2

MacromoleculeName: COP9 signalosome complex subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.66457 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDMEDDFMC DDEEDYDLEY SEDSNSEPNV DLENQYYNSK ALKEDDPKAA LSSFQKVLEL EGEKGEWGFK ALKQMIKINF KLTNFPEMM NRYKQLLTYI RSAVTRNYSE KSINSILDYI STSKQMDLLQ EFYETTLEAL KDAKNDRLWF KTNTKLGKLY L EREEYGKL ...String:
MSDMEDDFMC DDEEDYDLEY SEDSNSEPNV DLENQYYNSK ALKEDDPKAA LSSFQKVLEL EGEKGEWGFK ALKQMIKINF KLTNFPEMM NRYKQLLTYI RSAVTRNYSE KSINSILDYI STSKQMDLLQ EFYETTLEAL KDAKNDRLWF KTNTKLGKLY L EREEYGKL QKILRQLHQS CQTDDGEDDL KKGTQLLEIY ALEIQMYTAQ KNNKKLKALY EQSLHIKSAI PHPLIMGVIR EC GGKMHLR EGEFEKAHTD FFEAFKNYDE SGSPRRTTCL KYLVLANMLM KSGINPFDSQ EAKPYKNDPE ILAMTNLVSA YQN NDITEF EKILKTNHSN IMDDPFIREH IEELLRNIRT QVLIKLIKPY TRIHIPFISK ELNIDVADVE SLLVQCILDN TIHG RIDQV NQLLELDHQK RGGARYTALD KWTNQLNSLN QAVVSKLA

UniProtKB: COP9 signalosome complex subunit 2

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Macromolecule #2: COP9 signalosome complex subunit 4

MacromoleculeName: COP9 signalosome complex subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.322688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAAVRQDLA QLMNSSGSHK DLAGKYRQIL EKAIQLSGAE QLEALKAFVE AMVNENVSLV ISRQLLTDFC THLPNLPDST AKEIYHFTL EKIQPRVISF EEQVASIRQH LASIYEKEED WRNAAQVLVG IPLETGQKQY NVDYKLETYL KIARLYLEDD D PVQAEAYI ...String:
MAAAVRQDLA QLMNSSGSHK DLAGKYRQIL EKAIQLSGAE QLEALKAFVE AMVNENVSLV ISRQLLTDFC THLPNLPDST AKEIYHFTL EKIQPRVISF EEQVASIRQH LASIYEKEED WRNAAQVLVG IPLETGQKQY NVDYKLETYL KIARLYLEDD D PVQAEAYI NRASLLQNES TNEQLQIHYK VCYARVLDYR RKFIEAAQRY NELSYKTIVH ESERLEALKH ALHCTILASA GQ QRSRMLA TLFKDERCQQ LAAYGILEKM YLDRIIRGNQ LQEFAAMLMP HQKATTADGS SILDRAVIEH NLLSASKLYN NIT FEELGA LLEIPAAKAE KIASQMITEG RMNGFIDQID GIVHFETREA LPTWDKQIQS LCFQVNNLLE KISQTAPEWT AQAM EAQMA Q

UniProtKB: COP9 signalosome complex subunit 4

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Macromolecule #3: COP9 signalosome complex subunit 5

MacromoleculeName: COP9 signalosome complex subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.562719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAASGSGMAQ KTWELANNMQ EAQSIDEIYK YDKKQQQEIL AAKPWTKDHH YFKYCKISAL ALLKMVMHAR SGGNLAVMGL MLGKVDGET MIIMDSFALP VEGTETRVNA QAAAYEYMAA YIENAKQVGR LENAIGWYHS HPGYGCWLSG INVSTQMLNQ Q FQEPFVAV ...String:
MAASGSGMAQ KTWELANNMQ EAQSIDEIYK YDKKQQQEIL AAKPWTKDHH YFKYCKISAL ALLKMVMHAR SGGNLAVMGL MLGKVDGET MIIMDSFALP VEGTETRVNA QAAAYEYMAA YIENAKQVGR LENAIGWYHS HPGYGCWLSG INVSTQMLNQ Q FQEPFVAV VIDPTRTISA GKVNLGAFRT YPKGYKPPDE GPSEYQTIPL NKIEDFGVHC KQYYALEVSY FKSSLDRKLL EL LWNKYWV NTLSSSSLLT NADYTTGQVF DLSEKLEQSE AQLGRGSFML GLETHDRKSE DKLAKATRDS CKTTIEAIHG LMS QVIKDK LFNQINIS

UniProtKB: COP9 signalosome complex subunit 5

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Macromolecule #4: COP9 signalosome complex subunit 6

MacromoleculeName: COP9 signalosome complex subunit 6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.203398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAAAAAAAA TNGTGGSSGM EVDAAVVPSV MACGVTGSVS VALHPLVILN ISDHWIRMRS QEGRPVQVIG ALIGKQEGRN IEVMNSFEL LSHTVEEKII IDKEYYYTKE EQFKQVFKEL EFLGWYTTGG PPDPSDIHVH KQVCEIIESP LFLKLNPMTK H TDLPVSVF ...String:
MAAAAAAAAA TNGTGGSSGM EVDAAVVPSV MACGVTGSVS VALHPLVILN ISDHWIRMRS QEGRPVQVIG ALIGKQEGRN IEVMNSFEL LSHTVEEKII IDKEYYYTKE EQFKQVFKEL EFLGWYTTGG PPDPSDIHVH KQVCEIIESP LFLKLNPMTK H TDLPVSVF ESVIDIINGE ATMLFAELTY TLATEEAERI GVDHVARMTA TGSGENSTVA EHLIAQHSAI KMLHSRVKLI LE YVKASEA GEVPFNHEIL REAYALCHCL PVLSTDKFKT DFYDQCNDVG LMAYLGTITK TCNTMNQFVN KFNVLYDRQG IGR RMRGLF F

UniProtKB: COP9 signalosome complex subunit 6

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Macromolecule #5: COP9 signalosome complex subunit 7b

MacromoleculeName: COP9 signalosome complex subunit 7b / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.656928 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGEQKPSSN LLEQFILLAK GTSGSALTAL ISQVLEAPGV YVFGELLELA NVQELAEGAN AAYLQLLNLF AYGTYPDYIA NKESLPELS TAQQNKLKHL TIVSLASRMK CIPYSVLLKD LEMRNLRELE DLIIEAVYTD IIQGKLDQRN QLLEVDFCIG R DIRKKDIN ...String:
MAGEQKPSSN LLEQFILLAK GTSGSALTAL ISQVLEAPGV YVFGELLELA NVQELAEGAN AAYLQLLNLF AYGTYPDYIA NKESLPELS TAQQNKLKHL TIVSLASRMK CIPYSVLLKD LEMRNLRELE DLIIEAVYTD IIQGKLDQRN QLLEVDFCIG R DIRKKDIN NIVKTLHEWC DGCEAVLLGI EQQVLRANQY KENHNRTQQQ VEAEVTNIKK TLKATASSSA QEMEQQLAER EC PPHAEQR QPTKKMSKVK GLVSSRH

UniProtKB: COP9 signalosome complex subunit 7b

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Macromolecule #6: COP9 signalosome complex subunit 8

MacromoleculeName: COP9 signalosome complex subunit 8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.245543 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPVAVMAESA FSFKKLLDQC ENQELEAPGG IATPPVYGQL LALYLLHNDM NNARYLWKRI PPAIKSANSE LGGIWSVGQR IWQRDFPGI YTTINAHQWS ETVQPIMEAL RDATRRRAFA LVSQAYTSII ADDFAAFVGL PVEEAVKGIL EQGWQADSTT R MVLPRKPV ...String:
MPVAVMAESA FSFKKLLDQC ENQELEAPGG IATPPVYGQL LALYLLHNDM NNARYLWKRI PPAIKSANSE LGGIWSVGQR IWQRDFPGI YTTINAHQWS ETVQPIMEAL RDATRRRAFA LVSQAYTSII ADDFAAFVGL PVEEAVKGIL EQGWQADSTT R MVLPRKPV AGALDVSFNK FIPLSEPAPV PPIPNEQQLA RLTDYVAFLE N

UniProtKB: COP9 signalosome complex subunit 8

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Macromolecule #7: Cullin-5

MacromoleculeName: Cullin-5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.085297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATSNLLKNK GSLQFEDKWD FMRPIVLKLL RQESVTKQQW FDLFSDVHAV CLWDDKGPAK IHQALKEDIL EFIKQAQARV LSHQDDTAL LKAYIVEWRK FFTQCDILPK PFCQLEITLM GKQGSNKKSN VEDSIVRKLM LDTWNESIFS NIKNRLQDSA M KLVHAERL ...String:
MATSNLLKNK GSLQFEDKWD FMRPIVLKLL RQESVTKQQW FDLFSDVHAV CLWDDKGPAK IHQALKEDIL EFIKQAQARV LSHQDDTAL LKAYIVEWRK FFTQCDILPK PFCQLEITLM GKQGSNKKSN VEDSIVRKLM LDTWNESIFS NIKNRLQDSA M KLVHAERL GEAFDSQLVI GVRESYVNLC SNPEDKLQIY RDNFEKAYLD STERFYRTQA PSYLQQNGVQ NYMKYADAKL KE EEKRALR YLETRRECNS VEALMECCVN ALVTSFKETI LAECQGMIKR NETEKLHLMF SLMDKVPNGI EPMLKDLEEH IIS AGLADM VAAAETITTD SEKYVEQLLT LFNRFSKLVK EAFQDDPRFL TARDKAYKAV VNDATIFKLE LPLKQKGVGL KTQP ESKCP ELLANYCDML LRKTPLSKKL TSEEIEAKLK EVLLVLKYVQ NKDVFMRYHK AHLTRRLILD ISADSEIEEN MVEWL REVG MPADYVNKLA RMFQDIKVSE DLNQAFKEMH KNNKLALPAD SVNIKILNAG AWSRSSEKVF VSLPTELEDL IPEVEE FYK KNHSGRKLHW HHLMSNGIIT FKNEVGQYDL EVTTFQLAVL FAWNQRPREK ISFENLKLAT ELPDAELRRT LWSLVAF PK LKRQVLLYEP QVNSPKDFTE GTLFSVNQEF SLIKNAKVQK RGKINLIGRL QLTTERMREE ENEGIVQLRI LRTQEAII Q IMKMRKKISN AQLQTELVEI LKNMFLPQKK MIKEQIEWLI EHKYIRRDES DINTFIYMA

UniProtKB: Cullin-5

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Macromolecule #8: RING-box protein 2

MacromoleculeName: RING-box protein 2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.697436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVEDGEET CALASHSGSS GSKSGGDKMF SLKKWNAVAM WSWDVECDTC AICRVQVMDA CLRCQAENKQ EDCVVVWGEC NHSFHNCCM SLWVKQNNRC PLCQQDWVVQ RIGK

UniProtKB: RING-box protein 2

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Macromolecule #9: COP9 signalosome complex subunit 1

MacromoleculeName: COP9 signalosome complex subunit 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.606496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPLPVQVFNL QGAVEPMQID VDPQEDPQNA PDVNYVVENP SLDLEQYAAS YSGLMRIERL QFIADHCPTL RVEALKMALS FVQRTFNVD MYEEIHRKLS EATRSSLREL QNAPDAIPES GVEPPALDTA WVEATRKKAL LKLEKLDTDL KNYKGNSIKE S IRRGHDDL ...String:
MPLPVQVFNL QGAVEPMQID VDPQEDPQNA PDVNYVVENP SLDLEQYAAS YSGLMRIERL QFIADHCPTL RVEALKMALS FVQRTFNVD MYEEIHRKLS EATRSSLREL QNAPDAIPES GVEPPALDTA WVEATRKKAL LKLEKLDTDL KNYKGNSIKE S IRRGHDDL GDHYLDCGDL SNALKCYSRA RDYCTSAKHV INMCLNVIKV SVYLQNWSHV LSYVSKAEST PEIAEQRGER DS QTQAILT KLKCAAGLAE LAARKYKQAA KCLLLASFDH CDFPELLSPS NVAIYGGLCA LATFDRQELQ RNVISSSSFK LFL ELEPQV RDIIFKFYES KYASCLKMLD EMKDNLLLDM YLAPHVRTLY TQIRNRALIQ YFSPYVSADM HRMAAAFNTT VAAL EDELT QLILEGLISA RVDSHSKILY ARDVDQRSTT FEKSLLMGKE FQRRAKAMML RAAVLRNQIH VKSPPREGSQ GELTP ANSQ SRMSTNM

UniProtKB: COP9 signalosome complex subunit 1

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Macromolecule #10: COP9 signalosome complex subunit 3

MacromoleculeName: COP9 signalosome complex subunit 3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.924008 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASALEQFVN SVRQLSAQGQ MTQLCELINK SGELLAKNLS HLDTVLGALD VQEHSLGVLA VLFVKFSMPS VPDFETLFSQ VQLFISTCN GEHIRYATDT FAGLCHQLTN ALVERKQPLR GIGILKQAID KMQMNTNQLT SIHADLCQLC LLAKCFKPAL P YLDVDMMD ...String:
MASALEQFVN SVRQLSAQGQ MTQLCELINK SGELLAKNLS HLDTVLGALD VQEHSLGVLA VLFVKFSMPS VPDFETLFSQ VQLFISTCN GEHIRYATDT FAGLCHQLTN ALVERKQPLR GIGILKQAID KMQMNTNQLT SIHADLCQLC LLAKCFKPAL P YLDVDMMD ICKENGAYDA KHFLCYYYYG GMIYTGLKNF ERALYFYEQA ITTPAMAVSH IMLESYKKYI LVSLILLGKV QQ LPKYTSQ IVGRFIKPLS NAYHELAQVY STNNPSELRN LVNKHSETFT RDNNMGLVKQ CLSSLYKKNI QRLTKTFLTL SLQ DMASRV QLSGPQEAEK YVLHMIEDGE IFASINQKDG MVSFHDNPEK YNNPAMLHNI DQEMLKCIEL DERLKAMDQE ITVN PQFVQ KSMGSQEDDS GNKPSSYS

UniProtKB: COP9 signalosome complex subunit 3

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Macromolecule #11: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.086562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGGGGLR Q

UniProtKB: Ubiquitin-like protein NEDD8

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 239911
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: OTHER / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

4d10


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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