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- PDB-9o04: CryoEM structure of the FBXO42-CCDC6-PP2Ac degradasome -

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Basic information

Entry
Database: PDB / ID: 9o04
TitleCryoEM structure of the FBXO42-CCDC6-PP2Ac degradasome
Components
  • Coiled-coil domain-containing protein 6
  • F-box only protein 42
  • SKP1
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
KeywordsTRANSFERASE / E3 ligase / phosphatase / scaffolding
Function / homology
Function and homology information


Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / peptidyl-threonine dephosphorylation / protein serine/threonine phosphatase complex / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / peptidyl-threonine dephosphorylation / protein serine/threonine phosphatase complex / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / SCF ubiquitin ligase complex / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / negative regulation of glycolytic process through fructose-6-phosphate / mesoderm development / protein serine/threonine phosphatase activity / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of cell differentiation / regulation of microtubule polymerization / phosphoprotein phosphatase activity / regulation of G1/S transition of mitotic cell cycle / chromosome, centromeric region / DARPP-32 events / negative regulation of hippo signaling / ubiquitin-like ligase-substrate adaptor activity / protein dephosphorylation / Cyclin A/B1/B2 associated events during G2/M transition / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Resolution of Sister Chromatid Cohesion / meiotic cell cycle / RAF activation / RHO GTPases Activate Formins / negative regulation of canonical Wnt signaling pathway / Spry regulation of FGF signaling / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / structural constituent of cytoskeleton / response to lead ion / SH3 domain binding / tau protein binding / spindle pole / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / mitotic cell cycle / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoskeleton / intracellular signal transduction / membrane raft / protein heterodimerization activity / synapse / chromatin / mitochondrion / extracellular exosome / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
: / Protein of unknown function DUF2046 / Uncharacterized conserved protein H4 (DUF2046) / FBX42, beta-propeller domain / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / KLHDC2/KLHL20/DRC7 Kelch-repeats domain ...: / Protein of unknown function DUF2046 / Uncharacterized conserved protein H4 (DUF2046) / FBX42, beta-propeller domain / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / F-box domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Kelch-type beta propeller / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Coiled-coil domain-containing protein 6 / F-box only protein 42
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHsu, P.L. / Michaelian, N. / Azumaya, C. / Coassolo, S. / Yauch, R.L.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: The SCFFBXO42-CCDC6 axis regulates proteosomal degradation of the catalytic subunit of PP2A
Authors: Hsu, P.L. / Michaelian, N. / Azumaya, C. / Coassolo, S. / Yauch, R.L. / Maculins, T. / Dimitrova, Y.
History
DepositionApr 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil domain-containing protein 6
B: Coiled-coil domain-containing protein 6
C: F-box only protein 42
D: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
E: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
F: SKP1
G: F-box only protein 42
H: SKP1
I: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
J: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
K: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
L: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
M: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
N: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)606,64130
Polymers605,76214
Non-polymers87916
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 Coiled-coil domain-containing protein 6 / Papillary thyroid carcinoma-encoded protein / Protein H4


Mass: 55322.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC6, D10S170, TST1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16204
#2: Protein F-box only protein 42 / Just one F-box and Kelch domain-containing protein


Mass: 75126.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO42, FBX42, JFK, KIAA1332 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P3S6
#3: Protein
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 38858.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P67775, protein-serine/threonine phosphatase
#4: Protein SKP1


Mass: 16997.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN
Has protein modificationY

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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: Complex of FBXO42-CCDC6-PP2Ac / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES pH 7.5, 200 mM NaCl, 1 mM TCEP pH 7.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: coated with self assembled monolayers / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21534 / Details: 15.8 eps collected as 40 frame movies
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
9PHENIX1.20.1_4487model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7261626
Details: template picked from 2D classes in Glacios screening dataset
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155244 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00630047
ELECTRON MICROSCOPYf_angle_d1.35440723
ELECTRON MICROSCOPYf_dihedral_angle_d53991
ELECTRON MICROSCOPYf_chiral_restr0.0864362
ELECTRON MICROSCOPYf_plane_restr0.0115290

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