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- EMDB-53253: Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP... -

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Basic information

Entry
Database: EMDB / ID: EMD-53253
TitleActivated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure
Map data
Sample
  • Complex: COP9 signalosome and neddylated SCF complex
    • Complex: COP9 signalosome
      • Protein or peptide: x 9 types
    • Complex: Neddylated Cullin-1/Rbx1 complex
      • Complex: Cullin-1/Rbx1
        • Protein or peptide: x 2 types
      • Complex: Nedd8
        • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsCullin-RING E3 ligases / COP9 signalosome / LIGASE
Function / homology
Function and homology information


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 ...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 / 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 / protein K27-linked ubiquitination / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / negative regulation of protein neddylation / protein neddylation / NEDD8 ligase activity / Hydrolases; Acting on peptide bonds (peptidases) / RHOBTB1 GTPase cycle / metal-dependent deubiquitinase activity / VCB complex / negative regulation of response to oxidative stress / 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 / 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 / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / negative regulation of mitophagy / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / 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 / protein monoubiquitination / anatomical structure morphogenesis / site of DNA damage / : / protein K48-linked ubiquitination / signal transduction in response to DNA damage / 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 / negative regulation of canonical NF-kappaB signal transduction / animal organ morphogenesis / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of CRY and PER proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / cellular response to amino acid stimulus / protein modification process / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / 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 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / modification-dependent protein catabolic process
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 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 / : / Cullin alpha+beta domain / 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 / 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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsDing S / Clapperton JA / Maeots ME / Shaaban M / Enchev RI
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53253.png

Downloads & links

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Map

FileDownload / File: emd_53253.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0174
Minimum - Maximum-0.0016998514 - 2.0622568
Average (Standard dev.)0.0014978604 (±0.0264483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53253_half_map_1.map
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Half map: #1

Fileemd_53253_half_map_2.map
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Sample components

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Entire : COP9 signalosome and neddylated SCF complex

EntireName: COP9 signalosome and neddylated SCF complex
Components
  • Complex: COP9 signalosome and neddylated SCF complex
    • Complex: COP9 signalosome
      • 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: COP9 signalosome complex subunit 9
      • Protein or peptide: COP9 signalosome complex subunit 1
    • Complex: Neddylated Cullin-1/Rbx1 complex
      • Complex: Cullin-1/Rbx1
        • Protein or peptide: Cullin-1
        • Protein or peptide: E3 ubiquitin-protein ligase RBX1
      • Complex: Nedd8
        • Protein or peptide: NEDD8
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: COP9 signalosome and neddylated SCF complex

SupramoleculeName: COP9 signalosome and neddylated SCF complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#12, #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: COP9 signalosome

SupramoleculeName: COP9 signalosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#8, #11, #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Neddylated Cullin-1/Rbx1 complex

SupramoleculeName: Neddylated Cullin-1/Rbx1 complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Cullin-1/Rbx1

SupramoleculeName: Cullin-1/Rbx1 / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #9-#10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Nedd8

SupramoleculeName: Nedd8 / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #12
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: COP9 signalosome complex subunit 1

MacromoleculeName: COP9 signalosome complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.606496 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #2: COP9 signalosome complex subunit 2

MacromoleculeName: COP9 signalosome complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.66457 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #3: COP9 signalosome complex subunit 3

MacromoleculeName: COP9 signalosome complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.924008 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #4: COP9 signalosome complex subunit 4

MacromoleculeName: COP9 signalosome complex subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.322688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #5: COP9 signalosome complex subunit 5

MacromoleculeName: COP9 signalosome complex subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.554672 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAASGSGMAQ KTWELANNMQ EAQSIDEIYK YDKKQQQEIL AAKPWTKDHH YFKYCKISAL ALLKMVMHAR SGGNLEVMGL MLGKVDGET MIIMDSFALP VEGTETRVNA QAAAYEYMAA YIENAKQVGR LENAIGWYAS HPGYGCWLSG IDVSTQMLNQ Q FQEPFVAV ...String:
MAASGSGMAQ KTWELANNMQ EAQSIDEIYK YDKKQQQEIL AAKPWTKDHH YFKYCKISAL ALLKMVMHAR SGGNLEVMGL MLGKVDGET MIIMDSFALP VEGTETRVNA QAAAYEYMAA YIENAKQVGR LENAIGWYAS HPGYGCWLSG IDVSTQMLNQ 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 #6: COP9 signalosome complex subunit 6

MacromoleculeName: COP9 signalosome complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.203398 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #7: COP9 signalosome complex subunit 7b

MacromoleculeName: COP9 signalosome complex subunit 7b / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.656928 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #8: COP9 signalosome complex subunit 8

MacromoleculeName: COP9 signalosome complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.245543 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #9: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKDVFQKF YAKMLAKRLV HQNSA SDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVLSSGS WPFQQSCTFA LPSELE RSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAYTVQ QLTDSTQIKM DILAQVL QI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMKTEQ KQEQETTHKN IEEDRKLLIQ AAIVRIMK M RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

UniProtKB: Cullin-1

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Macromolecule #10: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

+
Macromolecule #11: COP9 signalosome complex subunit 9

MacromoleculeName: COP9 signalosome complex subunit 9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.213689 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MKPAVDEMFP EGAGPYVDLD EAGGSTGLLM DLAANEKAVH ADFFNDFEDL FDDDDIQ

UniProtKB: COP9 signalosome complex subunit 9

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Macromolecule #12: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.573978 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG

UniProtKB: Ubiquitin-like protein NEDD8

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Macromolecule #13: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 556830
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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