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- PDB-9kbd: Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition liga... -

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Basic information

Entry
Database: PDB / ID: 9kbd
TitleCryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
Components
  • Cullin-1
  • E3 ubiquitin-protein ligase RBX1
  • F-box only protein 3
  • S-phase kinase-associated protein 1
KeywordsLIGASE / ubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / positive regulation of ubiquitin protein ligase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus ...Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / positive regulation of ubiquitin protein ligase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein K27-linked ubiquitination / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / negative regulation of mitophagy / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / site of DNA damage / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / : / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / negative regulation of insulin receptor signaling pathway / intrinsic apoptotic signaling pathway / post-translational protein modification / molecular function activator activity / negative regulation of canonical NF-kappaB signal transduction / T cell activation / animal organ morphogenesis / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of CRY and PER proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / cellular response to amino acid stimulus / Vpu mediated degradation of CD4 / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / G1/S transition of mitotic cell cycle / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / 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 / beta-catenin binding / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / DNA Damage Recognition in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Dual Incision in GG-NER / SCF(Skp2)-mediated degradation of p27/p21 / 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 / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RAS by GAPs / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / positive regulation of protein catabolic process
Similarity search - Function
: / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile. / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / A Receptor for Ubiquitination Targets ...: / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile. / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / A Receptor for Ubiquitination Targets / : / Cullin alpha+beta domain / 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, N-terminal / Cullin alpha solenoid domain / Cullin / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / F-box only protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWei, J. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proteins / Year: 2025
Title: Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex.
Authors: Jiajia Wei / Chao Xu /
Abstract: The cryo-EM structure of human SCF, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ...The cryo-EM structure of human SCF, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3 is incorporated into the SCF complex remains elusive. In the cryo-EM structure of SCF, the F-box domain of FBXO3 primarily associates with SKP1 via extensive hydrophobic interactions and interacts with the N-terminal region of CUL1 via hydrophobic interactions. The weak cryo-EM map of the RBX1 globular region is close to the FBXO3 ApaG domain, suggesting that unmodified SCF exhibits a closed conformation and that CUL1 neddylation is likely required to achieve high E3 activity. The structural study provides insight into the assembly of SCF and its activation mediated by CUL1 neddylation.
History
DepositionOct 30, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: S-phase kinase-associated protein 1
C: F-box only protein 3
R: E3 ubiquitin-protein ligase RBX1
A: Cullin-1


Theoretical massNumber of molelcules
Total (without water)171,0764
Polymers171,0764
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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: 18679.965 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
#2: Protein F-box only protein 3


Mass: 50305.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO3, FBX3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK99
#3: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 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, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
#4: Protein Cullin-1 / CUL-1


Mass: 89800.367 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
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-FBXO3 SCF ubiquition ligase complex
Type: COMPLEX
Details: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
Entity ID: all / Source: RECOMBINANT
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: TFS 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
Image recordingElectron dose: 55.62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185300 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310945
ELECTRON MICROSCOPYf_angle_d0.57914786
ELECTRON MICROSCOPYf_dihedral_angle_d4.1941439
ELECTRON MICROSCOPYf_chiral_restr0.0421629
ELECTRON MICROSCOPYf_plane_restr0.0041898

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