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- EMDB-61550: Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition liga... -

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Basic information

Entry
Database: EMDB / ID: EMD-61550
TitleCryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
Map data
Sample
  • Complex: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
    • Protein or peptide: F-box only protein 4
    • Protein or peptide: Cullin-1
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
Keywordsubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / common myeloid progenitor cell proliferation / F-box domain binding / PcG protein complex / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cellular homeostasis / cullin-RING ubiquitin ligase complex ...positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / common myeloid progenitor cell proliferation / F-box domain binding / PcG protein complex / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cellular homeostasis / 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 / regulation of DNA damage checkpoint / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / ubiquitin ligase activator activity / NEDD8 ligase activity / protein K27-linked ubiquitination / negative regulation of response to oxidative stress / negative regulation of protein localization to nucleus / VCB complex / Cul5-RING ubiquitin ligase complex / post-transcriptional regulation of gene expression / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / 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 / Prolactin receptor signaling / negative regulation of mitophagy / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Association of TriC/CCT with target proteins during biosynthesis / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / ubiquitin ligase complex / negative regulation of fibroblast proliferation / ubiquitin-like ligase-substrate adaptor activity / site of DNA damage / signal transduction in response to DNA damage / positive regulation of telomere maintenance via telomerase / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / negative regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / post-translational protein modification / intrinsic apoptotic signaling pathway / telomere maintenance / molecular function activator activity / animal organ morphogenesis / T cell activation / positive regulation of protein ubiquitination / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cellular response to ionizing radiation / negative regulation of canonical NF-kappaB signal transduction / cellular response to amino acid stimulus / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / regulation of protein stability / negative regulation of canonical Wnt signaling pathway / Vpu mediated degradation of CD4 / G1/S transition of mitotic cell cycle / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of CRY and PER proteins / Iron uptake and transport / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / RING-type E3 ubiquitin transferase / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / beta-catenin binding / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / protein destabilization / NOTCH1 Intracellular Domain Regulates Transcription / Evasion by RSV of host interferon responses / Degradation of beta-catenin by the destruction complex / DNA Damage Recognition in GG-NER / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / CLEC7A (Dectin-1) signaling / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER)
Similarity search - Function
F-box only protein 4 / 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 ...F-box only protein 4 / 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, N-terminal / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin alpha solenoid domain / Cullin protein neddylation domain / Cullin / : / 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 / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / F-box only protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsZhu W / Xu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquitin ligase complex.
Authors: Wenjie Zhu / Xinyan Chen / Jiahai Zhang / Chao Xu /
Abstract: Cullin-RING E3 ubiquitin ligases (CRLs) constitute the largest family of ubiquitin ligase and play important roles in regulation of proteostasis. Here we presented the cryo-EM structure of CRL1, a ...Cullin-RING E3 ubiquitin ligases (CRLs) constitute the largest family of ubiquitin ligase and play important roles in regulation of proteostasis. Here we presented the cryo-EM structure of CRL1, a member of Cullin-1 E3 ligase. CRL1 adopts a homodimer architecture. Structural analysis revealed that in the CRL1 protomer, the substrate recognition subunit FBXO4 interacts both the adaptor protein SKP1, and the scaffold protein CUL1 via hydrophobic and electrostatic interactions. Two FBXO4 forms a domain-swapped dimer in the CRL1 structure, which constitutes the basis for the dimerization of CRL1. Inspired by the cryo-EM density, we modeled the architecture of whole CRL1 as a symmetrical dimer, which provides insights into CRL1-medaited turnover of oncogene proteins.
History
DepositionSep 15, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61550.png

Downloads & links

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Map

FileDownload / File: emd_61550.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0638
Minimum - Maximum-0.48149765 - 0.8627293
Average (Standard dev.)-0.000036920297 (±0.010325991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61550_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61550_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex

EntireName: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
Components
  • Complex: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
    • Protein or peptide: F-box only protein 4
    • Protein or peptide: Cullin-1
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed

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Supramolecule #1: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex

SupramoleculeName: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: F-box only protein 4

MacromoleculeName: F-box only protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.247145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HMEAASTLTR LPIDVQLYIL SFLSPHDLCQ LGSTNHYWNE TVRDPILWRY FLLRDLPSWS SVDWKSLPDL EILKKPISEV TDGAFFDYM AVYRMCCPYL IIQNEPRFAM FGPGLEELNT SLVLSLMSSE ELCPTAGLPQ RQIDGIGSGV NFQLNNQHKF N ILILYSTT ...String:
HMEAASTLTR LPIDVQLYIL SFLSPHDLCQ LGSTNHYWNE TVRDPILWRY FLLRDLPSWS SVDWKSLPDL EILKKPISEV TDGAFFDYM AVYRMCCPYL IIQNEPRFAM FGPGLEELNT SLVLSLMSSE ELCPTAGLPQ RQIDGIGSGV NFQLNNQHKF N ILILYSTT RKERDRAREE HTSAVNKMFS RHNEGDDQQG SRYSVIPQIQ KVCEVVDGFI YVANAEAHKR HEWQDEFSHI MA MTDPAFG SSGRPLLVLS CISQGDVKRM PCFYLAHELH LNLLNHPWLV QDTEAETLTG FLNGIEWILE EVESKRAR

UniProtKB: F-box only protein 4

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Macromolecule #2: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.715352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SASWSHPQFE KGGGSGGGSK LSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPP SKSKKGQTPG GAQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY L NRHWVRRE ...String:
SASWSHPQFE KGGGSGGGSK LSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPP SKSKKGQTPG GAQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY L NRHWVRRE CDEGRKGIYE IYSLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FA KGPTLTV YKESFESQFL ADTERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHL EIFHTE FQNLLDADKN EDLGRMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNAL VMSAF NNDAGFVAAL DKACGRFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKD VFQK FYAKMLAKRL VHQNSASDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVL SSG SWPFQQSCTF ALPSELERSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAY TV QQLTDSTQIK MDILAQVLQI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMKTEQ KQEQETTH K NIEEDRKLLI QAAIVRIMKM RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

UniProtKB: Cullin-1

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Macromolecule #3: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.881146 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGSMPSIKLQ SSDGEIFEVD VEIAKQSVTI KTMLEDLGMD DEGDDDPVPL PNVNAAILKK VIQWCTHHKD DPPPPEDDEN KEKRTDDIP VWDQEFLKVD QGTLFELILA ANYLDIKGLL DVTCKTVANM IKGKTPEEIR KTFNIKNDFT EEEEAQVRKE N QWCEEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #4: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.19683 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SHMGAGKKRF EVKKWNAVAL WAWDIVVDNC AICRNHIMDL CIECQANQAS ATSEECTVAW GVCNHAFHFH CISRWLKTRQ VCPLDNREW EFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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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 / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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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 K3 (6k x 4k) / Average electron dose: 55.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102037
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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