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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 / F-box domain binding / common myeloid progenitor cell proliferation / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / cellular response to chemical stress ...positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / common myeloid progenitor cell proliferation / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / cellular homeostasis / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / negative regulation of protein localization to nucleus / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / post-transcriptional regulation of gene expression / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / protein monoubiquitination / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / negative regulation of fibroblast proliferation / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / positive regulation of telomere maintenance via telomerase / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / telomere maintenance / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / Regulation of BACH1 activity / T cell activation / molecular function activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / animal organ morphogenesis / positive regulation of protein ubiquitination / cellular response to ionizing radiation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / cellular response to amino acid stimulus / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / 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 destabilization / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / beta-catenin binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / regulation of protein stability / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / CLEC7A (Dectin-1) signaling / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin
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, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / 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
AxesZYX

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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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