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- PDB-9jkb: Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition liga... -

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Basic information

Entry
Database: PDB / ID: 9jkb
TitleCryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
Components
  • Cullin-1
  • E3 ubiquitin-protein ligase RBX1, N-terminally processed
  • F-box only protein 4
  • S-phase kinase-associated protein 1
KeywordsPROTEIN BINDING / ubiquitination E3 ligase / Cryo-EM
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 / Cul7-RING ubiquitin ligase complex ...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 / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of DNA damage checkpoint / cellular response to chemical stress / 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 / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / post-transcriptional regulation of gene expression / Cul3-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / protein monoubiquitination / ubiquitin ligase complex / negative regulation of fibroblast proliferation / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of telomere maintenance via telomerase / transcription-coupled nucleotide-excision repair / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / telomere maintenance / post-translational protein modification / Regulation of BACH1 activity / molecular function activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T cell 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 / Negative regulation of NOTCH4 signaling / Recognition of DNA damage by PCNA-containing replication complex / Vif-mediated degradation of APOBEC3G / G1/S transition of mitotic cell cycle / Hedgehog 'on' state / negative regulation of canonical Wnt signaling pathway / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / beta-catenin binding / DNA Damage Recognition in GG-NER / protein destabilization / 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 / CLEC7A (Dectin-1) signaling / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / SCF(Skp2)-mediated degradation of p27/p21 / Formation of TC-NER Pre-Incision Complex / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsZhu, W. / Xu, C.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: F-box only protein 4
A: Cullin-1
B: S-phase kinase-associated protein 1
R: E3 ubiquitin-protein ligase RBX1, N-terminally processed
D: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)194,2885
Polymers194,2885
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein F-box only protein 4


Mass: 36247.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO4, FBX4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKT5
#2: Protein Cullin-1 / CUL-1


Mass: 91715.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#3: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18881.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208
#4: Protein E3 ubiquitin-protein ligase RBX1, N-terminally processed / E3 ubiquitin-protein transferase RBX1 / N-terminally processed


Mass: 11196.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
Type: COMPLEX
Details: Cryo-EM of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102037 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039716
ELECTRON MICROSCOPYf_angle_d0.66613132
ELECTRON MICROSCOPYf_dihedral_angle_d4.3171267
ELECTRON MICROSCOPYf_chiral_restr0.0431466
ELECTRON MICROSCOPYf_plane_restr0.0051685

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