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- EMDB-4742: Structural basis of Cullin-2 RING E3 ligase regulation by the COP... -

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Basic information

Entry
Database: EMDB / ID: EMD-4742
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: CSN-CRL2-N8
    • Protein or peptide: x 13 types
  • Ligand: x 2 types
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 / regulation of IRE1-mediated unfolded protein response / global genome nucleotide-excision repair / 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 / regulation of IRE1-mediated unfolded protein response / global genome nucleotide-excision repair / exosomal secretion / deNEDDylase activity / GTPase inhibitor 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 / cullin-RING ubiquitin ligase complex / COP9 signalosome / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / elongin complex / VCB complex / positive regulation of protein autoubiquitination / protein neddylation / metal-dependent deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases) / NEDD8 ligase activity / RHOBTB1 GTPase cycle / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / inner cell mass cell proliferation / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / TP53 Regulates Transcription of DNA Repair Genes / Prolactin receptor signaling / skeletal muscle cell differentiation / TGF-beta receptor signaling activates SMADs / 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 / response to light stimulus / anatomical structure morphogenesis / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein K48-linked ubiquitination / RNA Polymerase II Transcription Elongation / Nuclear events stimulated by ALK signaling in cancer / Formation of RNA Pol II elongation complex / response to UV / JNK cascade / RNA Polymerase II Pre-transcription Events / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / translation initiation factor activity / regulation of cellular response to insulin stimulus / Regulation of BACH1 activity / transcription corepressor binding / T cell activation / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / Degradation of DVL / cellular response to amino acid stimulus / Iron uptake and transport / transcription elongation by RNA polymerase II / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / positive regulation of DNA-binding transcription factor activity / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / protein modification process / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Inactivation of CSF3 (G-CSF) signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
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 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / COP9 signalosome complex subunit 1, C-terminal helix ...COP9 signalosome, subunit CSN8 / 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 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 complex subunit 4, helix turn helix domain / Cop9 signalosome subunit 5 C-terminal domain / CSN4/RPN5/eIF3a helix turn helix 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 / : / : / 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 / PCI/PINT associated module / Cullin protein neddylation domain / : / Elongin B / Elongin-C / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / 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 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 / Elongin-C / COP9 signalosome complex subunit 1 / Cullin-2 / Elongin-B / NEDD8 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 ...COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / Elongin-C / COP9 signalosome complex subunit 1 / Cullin-2 / Elongin-B / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsFaull SF / Lau AMC / Beuron F / Cronin NB / Morris EP / Politis A
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 28, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseAug 28, 2019-
UpdateSep 4, 2019-
Current statusSep 4, 2019Processing 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-6r7i
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4742.png

Downloads & links

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Map

FileDownload / File: emd_4742.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-12.318111 - 28.965525
Average (Standard dev.)0.000000007566055 (±1.0000001)
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-12.31828.9660.000

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Supplemental data

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Sample components

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Entire : CSN-CRL2-N8

EntireName: CSN-CRL2-N8
Components
  • Complex: CSN-CRL2-N8
    • 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-2
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: CSN-CRL2-N8

SupramoleculeName: CSN-CRL2-N8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 52.494109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KVYIEKDVEN PSLDLEQYAA SYSGLMRIER LQFIADHCPT LRVEALKMAL SFVQRTFNVD MYEEIHRKLS EATRSSLREL QNAPDAIPE SGVEPPALDT AWVEATRKKA LLKLEKLDTD LKNYKGNSIK ESIRRGHDDL GDHYLDCGDL SNALKCYSRA R DYCTSAKH ...String:
KVYIEKDVEN PSLDLEQYAA SYSGLMRIER LQFIADHCPT LRVEALKMAL SFVQRTFNVD MYEEIHRKLS EATRSSLREL QNAPDAIPE SGVEPPALDT AWVEATRKKA LLKLEKLDTD LKNYKGNSIK ESIRRGHDDL GDHYLDCGDL SNALKCYSRA R DYCTSAKH VINMCLNVIK VSVYLQNWSH VLSYVSKAES TPEIAEQRGE RDSQTQAILT KLKCAAGLAE LAARKYKQAA KC LLLASFD HCDFPELLSP SNVAIYGGLC ALATFDRQEL QRNVISSSSF KLFLELEPQV RDIIFKFYES KYASCLKMLD EMK DNLLLD MYLAPHVRTL YTQIRNRALI QYFSPYVSAD MHRMAAAFNT TVAALEDELT QLILEGLISA RVDSHSKILY ARDV DQRST TFEKSLLMGK EFQRRAKAMM LRAAVLRNQI HVKSPPREGS QGELTPANSQ SRMSTNM

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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

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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: 45.606543 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SALEQFVNSV RQLSAQGQMT QLCELINKSG ELLAKNLSHL DTVLGALDVQ EHSLGVLAVL FVKFSMPSVP DFETLFSQVQ LFISTCNGE HIRYATDTFA GLCHQLTNAL VERKQPLRGI GILKQAIDKM QMNTNQLTSI HADLCQLCLL AKCFKPALPY L DVDMMDIC ...String:
SALEQFVNSV RQLSAQGQMT QLCELINKSG ELLAKNLSHL DTVLGALDVQ EHSLGVLAVL FVKFSMPSVP DFETLFSQVQ LFISTCNGE HIRYATDTFA GLCHQLTNAL VERKQPLRGI GILKQAIDKM QMNTNQLTSI HADLCQLCLL AKCFKPALPY L DVDMMDIC KENGAYDAKH FLCYYYYGGM IYTGLKNFER ALYFYEQAIT TPAMAVSHIM LESYKKYILV SLILLGKVQQ LP KYTSQIV GRFIKPLSNA YHELAQVYST NNPSELRNLV NKHSETFTRD NNMGLVKQCL SSLYKKNIQR LTKTFLTLSL QDM ASRVQL SGPQEAEKYV LHMIEDGEIF ASINQKDGMV SFHDNPEKYN NPAMLHNIDQ EMLKCIELDE RLKAMDQEIT VNPQ F

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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: 46.479879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RMAAAVRQDL AQLMNSSGSH KDLAGKYRQI LEKAIQLSGA EQLEALKAFV EAMVNENVSL VISRQLLTDF CTHLPNLPDS TAKEIYHFT LEKIQPRVIS FEEQVASIRQ HLASIYEKEE DWRNAAQVLV GIPLETGQKQ YNVDYKLETY LKIARLYLED D DPVQAEAY ...String:
RMAAAVRQDL AQLMNSSGSH KDLAGKYRQI LEKAIQLSGA EQLEALKAFV EAMVNENVSL VISRQLLTDF CTHLPNLPDS TAKEIYHFT LEKIQPRVIS FEEQVASIRQ HLASIYEKEE DWRNAAQVLV GIPLETGQKQ YNVDYKLETY LKIARLYLED D DPVQAEAY INRASLLQNE STNEQLQIHY KVCYARVLDY RRKFIEAAQR YNELSYKTIV HESERLEALK HALHCTILAS AG QQRSRML ATLFKDERCQ QLAAYGILEK MYLDRIIRGN QLQEFAAMLM PHQKATTADG SSILDRAVIE HNLLSASKLY NNI TFEELG ALLEIPAAKA EKIASQMITE GRMNGFIDQI DGIVHFETRE ALPTWDKQIQ SLCFQVNNLL EKISQTAPEW TAQA MEAQM AQ

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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

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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

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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: 23.9444 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 DIRKKDLS ...String:
MAGEQKPSSN LLEQFILLAK GTSGSALTAL ISQVLEAPGV YVFGELLELA NVQELAEGAN AAYLQLLNLF AYGTYPDYIA NKESLPELS TAQQNKLKHL TIVSLASRMK CIPYSVLLKD LEMRNLRELE DLIIEAVYTD IIQGKLDQRN QLLEVDFCIG R DIRKKDLS AIARTLQEWC VGCEVVLSGI EEQVSRANQH KEQQLGLKQQ IESEVAN

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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

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Macromolecule #9: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.876831 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GS(MSE)LIKVKTL TGKEIEIDIE PTDKVERIKE RVEEKEGIPP QQQRLIYSGK Q(MSE)NDEKTAAD YKI(MSE)GGSV L HLVLALRGG

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Macromolecule #10: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 10 / 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

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Macromolecule #11: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.973649 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQ

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Macromolecule #12: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 12 / 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 #13: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.021553 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
KKKRFEVKKW NAVALWAWDI VVDNCAICRN HIMDLCIECQ ANQASATSEE CTVAWGVCNH AFHFHCISRW LKTRQVCPLD NREWE

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #15: water

MacromoleculeName: water / type: ligand / ID: 15 / Number of copies: 169 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 75.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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 correctionSoftware - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 316921
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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