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- EMDB-14547: Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for m... -

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Entry
Database: EMDB / ID: EMD-14547
TitleStructure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation
Map data
Sample
  • Complex: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
    • Protein or peptide: Cullin-7
    • Protein or peptide: F-box/WD repeat-containing protein 8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: S-phase kinase-associated protein 1
  • Ligand: ZINC ION
KeywordsCullin-RING Ubiquitin E3 Ligase / LIGASE
Function / homology
Function and homology information


3M complex / anaphase-promoting complex / F-box domain binding / PcG protein complex / XBP1(S) activates chaperone genes / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / maintenance of protein location in nucleus ...3M complex / anaphase-promoting complex / F-box domain binding / PcG protein complex / XBP1(S) activates chaperone genes / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of dendrite morphogenesis / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / ubiquitin ligase activator activity / NEDD8 ligase activity / labyrinthine layer blood vessel development / protein K27-linked ubiquitination / negative regulation of response to oxidative stress / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of mitotic nuclear division / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / negative regulation of mitophagy / Cul4B-RING E3 ubiquitin ligase complex / Golgi organization / ubiquitin ligase complex scaffold activity / mitotic cytokinesis / cilium assembly / epithelial to mesenchymal transition / cullin family protein binding / protein monoubiquitination / vasculogenesis / ubiquitin-like ligase-substrate adaptor activity / site of DNA damage / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / protein K48-linked ubiquitination / negative regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / molecular function activator activity / placenta development / T cell activation / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of canonical NF-kappaB signal transduction / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / centriole / cellular response to amino acid stimulus / Vpu mediated degradation of CD4 / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / 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 / Recognition of DNA damage by PCNA-containing replication complex / Hedgehog 'on' state / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / RING-type E3 ubiquitin transferase / beta-catenin binding / Degradation of beta-catenin by the destruction complex / DNA Damage Recognition in GG-NER / NOTCH1 Intracellular Domain Regulates Transcription / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / CLEC7A (Dectin-1) signaling / microtubule cytoskeleton organization / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SCF(Skp2)-mediated degradation of p27/p21 / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / FCERI mediated NF-kB activation / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER
Similarity search - Function
: / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. ...: / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Quinoprotein alcohol dehydrogenase-like superfamily / SKP1/BTB/POZ domain superfamily / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Ribosomal protein L2, domain 2 / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-7 / F-box/WD repeat-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHopf LVM / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016European Union
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structure of CRL7 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation.
Authors: Linus V M Hopf / Kheewoong Baek / Maren Klügel / Susanne von Gronau / Yue Xiong / Brenda A Schulman /
Abstract: Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). ...Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). However, the vertebrate-specific CRL7 is of interest because it eludes existing models, yet its constituent cullin CUL7 and F-box protein FBXW8 are essential for development, and CUL7 mutations cause 3M syndrome. In this study, cryo-EM and biochemical analyses reveal the CRL7 assembly. CUL7's exclusivity for FBXW8 among all F-box proteins is explained by its unique F-box-independent binding mode. In CRL7, the RBX1 (also known as ROC1) RING domain is constrained in an orientation incompatible with binding E2~NEDD8 or E2~ubiquitin intermediates. Accordingly, purified recombinant CRL7 lacks auto-neddylation and ubiquitination activities. Instead, our data indicate that CRL7 serves as a substrate receptor linked via SKP1-FBXW8 to a neddylated CUL1-RBX1 catalytic module mediating ubiquitination. The structure reveals a distinctive CRL-CRL partnership, and provides a framework for understanding CUL7 assemblies safeguarding human health.
History
DepositionMar 17, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14547.png

Downloads & links

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Map

FileDownload / File: emd_14547.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
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Contour LevelBy AUTHOR: 0.0129
Minimum - Maximum-0.02152804 - 0.06922655
Average (Standard dev.)0.000057327103 (±0.0018496583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.86078 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14547_msk_1.map
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Additional map: #1

Fileemd_14547_additional_1.map
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Half map: #1

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Half map: #2

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Sample components

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Entire : Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex

EntireName: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
Components
  • Complex: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
    • Protein or peptide: Cullin-7
    • Protein or peptide: F-box/WD repeat-containing protein 8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: S-phase kinase-associated protein 1
  • Ligand: ZINC ION

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Supramolecule #1: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex

SupramoleculeName: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-7

MacromoleculeName: Cullin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 191.564359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMVGELRYR EFRVPLGPGL HAYPDELIRQ RVGHDGHPEY QIRWLILRRG DEGDGGSGQV DCKAEHILLW MSKDEIYANC HKMLGEDGQ VIGPSQESAG EVGALDKSVL EEMETDVKSL IQRALRQLEE CVGTIPPAPL LHTVHVLSAY ASIEPLTGVF K DPRVLDLL ...String:
GPMVGELRYR EFRVPLGPGL HAYPDELIRQ RVGHDGHPEY QIRWLILRRG DEGDGGSGQV DCKAEHILLW MSKDEIYANC HKMLGEDGQ VIGPSQESAG EVGALDKSVL EEMETDVKSL IQRALRQLEE CVGTIPPAPL LHTVHVLSAY ASIEPLTGVF K DPRVLDLL MHMLSSPDYQ IRWSAGRMIQ ALSSHDAGTR TQILLSLSQQ EAIEKHLDFD SRCALLALFA QATLSEHPMS FE GIQLPQV PGRVLFSLVK RYLHVTSLLD QLNDSAAEPG AQNTSAPEEL SGERGQLELE FSMAMGTLIS ELVQAMRWDQ ASD RPRSSA RSPGSIFQPQ LADVSPGLPA AQAQPSFRRS RRFRPRSEFA SGNTYALYVR DTLQPGMRVR MLDDYEEISA GDEG EFRQS NNGVPPVQVF WESTGRTYWV HWHMLEILGF EEDIEDMVEA DEYQGAVASR VLGRALPAWR WRPMTELYAV PYVLP EDED TEECEHLTLA EWWELLFFIK KLDGPDHQEV LQILQENLDG EILDDEILAE LAVPIELAQD LLLTLPQRLN DSALRD LIN CHVYKKYGPE ALAGNQAYPS LLEAQEDVLL LDAQAQAKDS EDAAKVEAKE PPSQSPNTPL QRLVEGYGPA GKILLDL EQ ALSSEGTQEN KVKPLLLQLQ RQPQPFLALM QSLDTPETNR TLHLTVLRIL KQLVDFPEAL LLPWHEAVDA CMACLRSP N TDREVLQELI FFLHRLTSVS RDYAVVLNQL GARDAISKAL EKHLGKLELA QELRDMVFKC EKHAHLYRKL ITNILGGCI QMVLGQIEDH RRTHRPINIP FFDVFLRYLC QGSSVEVKED KCWEKVEVSS NPHRASKLTD HNPKTYWESN GSAGSHYITL HMRRGILIR QLTLLVASED SSYMPARVVV CGGDSTSSLH TELNSVNVMP SASRVILLEN LTRFWPIIQI RIKRCQQGGI D TRIRGLEI LGPKPTFWPV FREQLCRHTR LFYMVRAQAW SQDMAEDRRS LLHLSSRLNG ALRQEQNFAD RFLPDDEAAQ AL GKTCWEA LVSPVVQNIT SPDEDGISPL GWLLDQYLEC QEAVFNPQSR GPAFFSRVRR LTHLLVHVEP CEAPPPVVAT PRP KGRNRS HDWSSLATRG LPSSIMRNLT RCWRAVVEKQ VNNFLTSSWR DDDFVPRYCE HFNILQNSSS ELFGPRAAFL LALQ NGCAG ALLKLPFLKA AHVSEQFARH IDQQIQGSRI GGAQEMERLA QLQQCLQAVL IFSGLEIATT FEHYYQHYMA DRLLG VVSS WLEGAVLEQI GPCFPNRLPQ QMLQSLSTSK ELQRQFHVYQ LQQLDQELLK LEDTEKKIQV GLGASGKEHK SEKEEE AGA AAVVDVAEGE EEEEENEDLY YEGAMPEVSV LVLSRHSWPV ASICHTLNPR TCLPSYLRGT LNRYSNFYNK SQSHPAL ER GSQRRLQWTW LGWAELQFGN QTLHVSTVQM WLLLYLNDLK AVSVESLLAF SGLSADMLNQ AIGPLTSSRG PLDLHEQK D IPGGVLKIRD GSKEPRSRWD IVRLIPPQTY LQAEGEDGQN LEKRRNLLNC LIVRILKAHG DEGLHIDQLV CLVLEAWQK GPCPPRGLVS SLGKGSACSS TDVLSCILHL LGKGTLRRHD DRPQVLSYAV PVTVMEPHTE SLNPGSSGPN PPLTFHTLQI RSRGVPYAS CTATQSFSTF R

UniProtKB: Cullin-7

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Macromolecule #2: F-box/WD repeat-containing protein 8

MacromoleculeName: F-box/WD repeat-containing protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.628852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMDDYSLDE FRRRWQEELA QAQAPKKRRR PEAAERRARR PEVGSGRGEQ ASGDPALAQR LLEGAGRPPA ARATRAEGQD VASRSRSPL AREGAGGGEQ LVDQLIRDLN EMNDVPFFDI QLPYELAINI FQYLDRKELG RCAQVSKTWK VIAEDEVLWY R LCQQEGHL ...String:
GPMDDYSLDE FRRRWQEELA QAQAPKKRRR PEAAERRARR PEVGSGRGEQ ASGDPALAQR LLEGAGRPPA ARATRAEGQD VASRSRSPL AREGAGGGEQ LVDQLIRDLN EMNDVPFFDI QLPYELAINI FQYLDRKELG RCAQVSKTWK VIAEDEVLWY R LCQQEGHL PDSSISDYSC WKLIFQECRA KEHMLRTNWK NRKGAVSELE HVPDTVLCDV HSHDGVVIAG YTSGDVRVWD TR TWDYVAP FLESEDEEDE PGMQPNVSFV RINSSLAVAA YEDGFLNIWD LRTGKYPVHR FEHDARIQAL ALSQDDATVA TAS AFDVVM LSPNEEGYWQ IAAEFEVPKL VQYLEIVPET RRYPVAVAAA GDLMYLLKAE DSARTLLYAH GPPVTCLDVS ANQV AFGVQ GLGWVYEGSK ILVYSLEAGR RLLKLGNVLR DFTCVNLSDS PPNLMVSGNM DGRVRIHDLR SGNIALSLSA HQLRV SAVQ MDDWKIVSGG EEGLVSVWDY RMNQKLWEVY SGHPVQHISF SSHSLITANV PYQTVMRNAD LDSFTTHRRH RGLIRA YEF AVDQLAFQSP LPVCRSSCDA MATHYYDLAL AFPYNHV

UniProtKB: F-box/WD repeat-containing protein 8

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Macromolecule #3: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 3 / 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: Homo sapiens (human)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #4: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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

Concentration1.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 355547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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