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- EMDB-4736: Structural basis of Cullin-2 RING E3 ligase regulation by the COP... -

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Basic information

Entry
Database: EMDB / ID: EMD-4736
TitleStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Map dataStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Sample
  • Complex: Cullin-Ring E3 Ligases (CRLs) complexes with neddylated COP9 signalosome (CSN)
    • Protein or peptide: x 13 types
  • Ligand: x 1 types
KeywordsCullin-Ring E3 Ligase COP9 Signalosome Neddylation / LIGASE
Function / homology
Function and homology information


nucleotide-excision repair factor 4 complex / regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / global genome nucleotide-excision repair / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity ...nucleotide-excision repair factor 4 complex / regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / global genome nucleotide-excision repair / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / protein deneddylation / regulation of cellular response to hypoxia / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / RHOBTB3 ATPase cycle / cullin-RING ubiquitin ligase complex / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / COP9 signalosome / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / activation of NF-kappaB-inducing kinase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / VCB complex / positive regulation of protein autoubiquitination / protein neddylation / metal-dependent deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases) / Replication of the SARS-CoV-1 genome / NEDD8 ligase activity / RHOBTB1 GTPase cycle / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / inner cell mass cell proliferation / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / intracellular non-membrane-bounded organelle / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / TP53 Regulates Transcription of DNA Repair Genes / SUMOylation of ubiquitinylation proteins / protein deubiquitination / Prolactin receptor signaling / negative regulation of transcription elongation by RNA polymerase II / skeletal muscle cell differentiation / protein monoubiquitination / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / regulation of JNK cascade / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / response to light stimulus / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / JNK cascade / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / T cell activation / translation initiation factor activity / Regulation of BACH1 activity / negative regulation of autophagy / intrinsic apoptotic signaling pathway / post-translational protein modification / transcription corepressor binding / Degradation of DVL / transcription elongation by RNA polymerase II / nucleotide-excision repair / positive regulation of cell differentiation / Recognition of DNA damage by PCNA-containing replication complex / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / cellular response to amino acid stimulus / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome
Similarity search - Function
COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 3-like, C-terminal helix / COP9 signalosome subunit 6 / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain ...COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 3-like, C-terminal helix / COP9 signalosome subunit 6 / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain / Cop9 signalosome subunit 5 C-terminal domain / CSN4/RPN5/eIF3a helix turn helix domain / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Elongin B / Cullin / Elongin-C / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Cullin / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Proteasome component (PCI) domain / PCI domain profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / 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
von Hippel-Lindau disease tumor suppressor / COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / Elongin-C / COP9 signalosome complex subunit 1 / Cullin-2 / Elongin-B / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 ...von Hippel-Lindau disease tumor suppressor / COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / Elongin-C / COP9 signalosome complex subunit 1 / Cullin-2 / Elongin-B / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsMorris EP / Faull SV
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.
Authors: Sarah V Faull / Andy M C Lau / Chloe Martens / Zainab Ahdash / Kjetil Hansen / Hugo Yebenes / Carla Schmidt / Fabienne Beuron / Nora B Cronin / Edward P Morris / Argyris Politis /
Abstract: Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. ...Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members.
History
DepositionMar 27, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseAug 28, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r6h
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4736.png

Downloads & links

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Map

FileDownload / File: emd_4736.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-5.7485147 - 20.682364
Average (Standard dev.)0.0000000391578 (±1.0000014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.000318.000318.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ132132232
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-5.74920.6820.000

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Supplemental data

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Sample components

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Entire : Cullin-Ring E3 Ligases (CRLs) complexes with neddylated COP9 sign...

EntireName: Cullin-Ring E3 Ligases (CRLs) complexes with neddylated COP9 signalosome (CSN)
Components
  • Complex: Cullin-Ring E3 Ligases (CRLs) complexes with neddylated COP9 signalosome (CSN)
    • 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 8
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-B
    • Protein or peptide: ELOC_HUMAN
    • Protein or peptide: RBX1_HUMAN
    • Protein or peptide: von Hippel-Lindau disease tumor suppressor
    • Protein or peptide: COP9 signalosome complex subunit 7b
  • Ligand: ZINC ION

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Supramolecule #1: Cullin-Ring E3 Ligases (CRLs) complexes with neddylated COP9 sign...

SupramoleculeName: Cullin-Ring E3 Ligases (CRLs) complexes with neddylated COP9 signalosome (CSN)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
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: 45.808816 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 PQF

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: 37.621742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAASGSGMAQ KTWELANNMQ EAQSIDEIYK YDKKQQQEIL AAKPWTKDHH YFKYCKISAL ALLKMVMHAR SGGNLEVMGL MLGKVDGET MIIMDSFALP VEGTETRVNA QAAAYEYMAA YIENAKQVGR LENAIGWYHS HPGYGCWLSG IDVSTQMLNQ Q FQEPFVAV ...String:
MAASGSGMAQ KTWELANNMQ EAQSIDEIYK YDKKQQQEIL AAKPWTKDHH YFKYCKISAL ALLKMVMHAR SGGNLEVMGL MLGKVDGET MIIMDSFALP VEGTETRVNA QAAAYEYMAA YIENAKQVGR LENAIGWYHS 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: 34.713844 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEVDAAVVPS VMACGVTGSV SVALHPLVIL NISDHWIRMR SQEGRPVQVI GALIGKQEGR NIEVMNSFEL LSHTVEEKII IDKEYYYTK EEQFKQVFKE LEFLGWYTTG GPPDPSDIHV HKQVCEIIES PLFLKLNPMT KHTDLPVSVF ESVIDIINGE A TMLFAELT ...String:
MEVDAAVVPS VMACGVTGSV SVALHPLVIL NISDHWIRMR SQEGRPVQVI GALIGKQEGR NIEVMNSFEL LSHTVEEKII IDKEYYYTK EEQFKQVFKE LEFLGWYTTG GPPDPSDIHV HKQVCEIIES PLFLKLNPMT KHTDLPVSVF ESVIDIINGE A TMLFAELT YTLATEEAER IGVDHVARMT ATGSGENSTV AEHLIAQHSA IKMLHSRVKL ILEYVKASEA GEVPFNHEIL RE AYALCHC LPVLSTDKFK TDFYDQCNDV GLMAYLGTIT KTCNTMNQFV NKFNVLYDRQ GIGRRMRGLF F

UniProtKB: COP9 signalosome complex subunit 6

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Macromolecule #7: COP9 signalosome complex subunit 8

MacromoleculeName: COP9 signalosome complex subunit 8 / type: protein_or_peptide / ID: 7 / 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 #8: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.09893 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK ...String:
MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK NDRGGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLTETGEY YKQEASNLLQ ESNCSQYMEK VL GRLKDEE IRCRKYLHPS SYTKVIHECQ QRMVADHLQF LHAECHNIIR QEKKNDMANM YVLLRAVSTG LPHMIQELQN HIH DEGLRA TSNLTQENMP TLFVESVLEV HGKFVQLINT VLNGDQHFMS ALDKALTSVV NYREPKSVCK APELLAKYCD NLLK KSAKG MTENEVEDRL TSFITVFKYI DDKDVFQKFY ARMLAKRLIH GLSMSMDSEE AMINKLKQAC GYEFTSKLHR MYTDM SVSA DLNNKFNNFI KNQDTVIDLG ISFQIYVLQA GAWPLTQAPS STFAIPQELE KSVQMFELFY SQHFSGRKLT WLHYLC TGE VKMNYLGKPY VAMVTTYQMA VLLAFNNSET VSYKELQDST QMNEKELTKT IKSLLDVKMI NHDSEKEDID AESSFSL NM NFSSKRTKFK ITTSMQKDTP QEMEQTRSAV DEDRKMYLQA AIVRIMKARK VLRHNALIQE VISQSRARFN PSISMIKK C IEVLIDKQYI ERSQASADEY SYVA

UniProtKB: Cullin-2

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Macromolecule #9: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.819483 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKA

UniProtKB: Elongin-B

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Macromolecule #10: ELOC_HUMAN

MacromoleculeName: ELOC_HUMAN / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.33876 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSQDFVTLVS KDDKEYEISR SAAMISPTLK AMIEGPFRES KGRIELKQFD SHILEKAVEY LNYNLKYSGV SEDDDEIPEF EIPTEMSLE LLLAADYLSI

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Macromolecule #11: RBX1_HUMAN

MacromoleculeName: RBX1_HUMAN / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.092631 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
AKKKRFEVKK WNAVALWAWD IVVDNCAICR NHIMDLCIEC QANQASATSE ECTVAWGVCN HAFHFHCISR WLKTRQVCPL DNREWE

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Macromolecule #12: von Hippel-Lindau disease tumor suppressor

MacromoleculeName: von Hippel-Lindau disease tumor suppressor / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.330764 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
RPVLRSVNSR EPSQVIFCNR SPRVVLPVWL NFDGEPQPYP TLPPGTGRRI HSYRGHLWLF RDAGTHDGLL VNQTELFVPS LNVDGQPIF ANITLPVYTL KERCLQVVRS LVKPENYRRL DIVRSLYEDL EDHPNVQKDL ERLTQERIAA A

UniProtKB: von Hippel-Lindau disease tumor suppressor

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Macromolecule #13: COP9 signalosome complex subunit 7b

MacromoleculeName: COP9 signalosome complex subunit 7b / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.228529 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SNLLEQFILL AKGTSGSALT ALISQVLEAP GVYVFGELLE LANVQELAEG ANAAYLQLLN LFAYGTYPDY IANKESLPEL STAQQNKLK HLTIVSLASR MKCIPYSVLL KDLEMRNLRE LEDLIIEAVY TDIIQGKLDQ RNQLLEVDFC IGRDIRKKDI N NIVKTLHE ...String:
SNLLEQFILL AKGTSGSALT ALISQVLEAP GVYVFGELLE LANVQELAEG ANAAYLQLLN LFAYGTYPDY IANKESLPEL STAQQNKLK HLTIVSLASR MKCIPYSVLL KDLEMRNLRE LEDLIIEAVY TDIIQGKLDQ RNQLLEVDFC IGRDIRKKDI N NIVKTLHE WCDGCEAVLL GIEQQVLRAN QYKENHNRTQ QQVEAEVT

UniProtKB: COP9 signalosome complex subunit 7b

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 1 / 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
Details: 15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 47170
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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24040
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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