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- EMDB-49966: CryoEM structure of the FBXO42-CCDC6-PP2Ac degradasome -

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Basic information

Entry
Database: EMDB / ID: EMD-49966
TitleCryoEM structure of the FBXO42-CCDC6-PP2Ac degradasome
Map data
Sample
  • Complex: Complex of FBXO42-CCDC6-PP2Ac
    • Protein or peptide: Coiled-coil domain-containing protein 6
    • Protein or peptide: F-box only protein 42
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: SKP1
  • Ligand: MANGANESE (II) ION
KeywordsE3 ligase / phosphatase / scaffolding / TRANSFERASE
Function / homology
Function and homology information


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 / peptidyl-threonine dephosphorylation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A 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 ...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 / peptidyl-threonine dephosphorylation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A 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 / Co-stimulation by CD28 / regulation of growth / RNA polymerase II transcription initiation surveillance / Disassembly of the destruction complex and recruitment of AXIN to the membrane / protein dephosphorylation / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / SCF ubiquitin ligase complex / protein-serine/threonine phosphatase / ERK/MAPK targets / negative regulation of glycolytic process through fructose-6-phosphate / vascular endothelial cell response to oscillatory fluid shear stress / mesoderm development / protein serine/threonine phosphatase activity / T cell homeostasis / positive regulation of NLRP3 inflammasome complex assembly / regulation of cell differentiation / regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / chromosome, centromeric region / DARPP-32 events / negative regulation of hippo signaling / Cyclin A/B1/B2 associated events during G2/M transition / ubiquitin-like ligase-substrate adaptor activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / phosphoprotein phosphatase activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / protein tyrosine phosphatase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Resolution of Sister Chromatid Cohesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / meiotic cell cycle / RAF activation / negative regulation of canonical Wnt signaling pathway / RHO GTPases Activate Formins / Spry regulation of FGF signaling / SH3 domain binding / PKR-mediated signaling / structural constituent of cytoskeleton / response to lead ion / Degradation of beta-catenin by the destruction complex / tau protein binding / spindle pole / Cyclin D associated events in G1 / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / microtubule cytoskeleton / cytoskeleton / intracellular signal transduction / membrane raft / protein heterodimerization activity / synapse / chromatin / mitochondrion / extracellular exosome / membrane / metal ion binding / identical protein binding / nucleus / 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 / F-box 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHsu PL / Michaelian N / Azumaya C / Coassolo S / Yauch RL
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2026
Title: Template-driven scaffolding of SCF regulates PP2A degradation.
Authors: Sebastien Coassolo / Nairie Michaelian / Timurs Maculins / Caleigh M Azumaya / Tommy K Cheung / Jianping Yin / Inna Zilberleyb / Kanika Bajaj Pahuja / Thomas Garner / Ted Lau / Davis Mau / ...Authors: Sebastien Coassolo / Nairie Michaelian / Timurs Maculins / Caleigh M Azumaya / Tommy K Cheung / Jianping Yin / Inna Zilberleyb / Kanika Bajaj Pahuja / Thomas Garner / Ted Lau / Davis Mau / Matthew Grimmer / Jean-Philippe Fortin / Mike Costa / Yoana N Dimitrova / Christopher M Rose / Peter L Hsu / Robert L Yauch /
Abstract: Protein phosphatase 2A (PP2A) is a Ser/Thr phosphatase that regulates the phosphorylation of almost all cellular processes, including cell division and proliferation. PP2A forms heterotrimeric ...Protein phosphatase 2A (PP2A) is a Ser/Thr phosphatase that regulates the phosphorylation of almost all cellular processes, including cell division and proliferation. PP2A forms heterotrimeric holoenzyme complexes comprising a catalytic subunit (PP2Ac), a scaffolding subunit (PP2Aa) and variable B regulatory subunits that exert precise control over enzyme substrate specificity and prevent indiscriminate dephosphorylation of phosphoproteins. However, the mechanisms that control the activity of uncomplexed catalytic subunits have remained relatively unclear. Here we find that the E3 ligase SKP1-CUL1-F-box (SCF) complex containing F-box other protein 42 (FBXO42, also known as JFK; hereafter, SCF) degrades holoenzyme-free PP2Ac in a complex with the coiled-coil protein CCDC6 to maintain cancer cell fitness. The cryo-electron microscopy structure of the FBXO42-CCDC6-PP2Ac assembly reveals a pseudosymmetric architecture in which CCDC6 forms a central dimeric template that recruits multiple copies of PP2Ac and creates a substrate for FBXO42. Both the quaternary structure of this CCDC6-PP2Ac heterodimer and the post-translationally methylated tail of PP2Ac are recognized by FBXO42 for ubiquitination. The multivalent structure facilitated by CCDC6 enables the assembly of multiple degradation complexes along a single coiled coil, leading to the turnover of free phosphatases and downregulation of catalytic activity. Together, our findings define a mechanism for PP2A control through the ubiquitin-proteosome system and establish a paradigm for cullin-RING ligase-substrate interactions.
History
DepositionApr 2, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49966.png

Downloads & links

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Map

FileDownload / File: emd_49966.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 480 pix.
= 402.24 Å		0.84 Å/pix.
x 480 pix.
= 402.24 Å		0.84 Å/pix.
x 480 pix.
= 402.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.838 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.7
Minimum - Maximum-41.313656000000002 - 60.354179999999999
Average (Standard dev.)0.004659253 (±1.0673391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 402.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focused refinement of PP2Ac repeat 1

Fileemd_49966_additional_1.map
Annotationfocused refinement of PP2Ac repeat 1
Projections & Slices
AxesZYX

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Additional map: focused refinement of PP2Ac repeat 3

Fileemd_49966_additional_10.map
Annotationfocused refinement of PP2Ac repeat 3
Projections & Slices
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Additional map: focused refinement of PP2Ac repeat 1 and 2

Fileemd_49966_additional_2.map
Annotationfocused refinement of PP2Ac repeat 1 and 2
Projections & Slices
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Additional map: consensus map of complex

Fileemd_49966_additional_3.map
Annotationconsensus map of complex
Projections & Slices
AxesZYX

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Additional map: PP2Ac repeat0, 1, 2

Fileemd_49966_additional_4.map
AnnotationPP2Ac repeat0, 1, 2
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Additional map: PP2Ac repeat0, 1

Fileemd_49966_additional_5.map
AnnotationPP2Ac repeat0, 1
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Additional map: PP2Ac repeat1 1FBXO42

Fileemd_49966_additional_6.map
AnnotationPP2Ac repeat1 1FBXO42
Projections & Slices
AxesZYX

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Additional map: PP2Ac repeat0

Fileemd_49966_additional_7.map
AnnotationPP2Ac repeat0
Projections & Slices
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Additional map: PP2Ac repeat1 2FBXO42

Fileemd_49966_additional_8.map
AnnotationPP2Ac repeat1 2FBXO42
Projections & Slices
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Additional map: focused refinement of PP2Ac repeat 2

Fileemd_49966_additional_9.map
Annotationfocused refinement of PP2Ac repeat 2
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Sample components

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Entire : Complex of FBXO42-CCDC6-PP2Ac

EntireName: Complex of FBXO42-CCDC6-PP2Ac
Components
  • Complex: Complex of FBXO42-CCDC6-PP2Ac
    • Protein or peptide: Coiled-coil domain-containing protein 6
    • Protein or peptide: F-box only protein 42
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: SKP1
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Complex of FBXO42-CCDC6-PP2Ac

SupramoleculeName: Complex of FBXO42-CCDC6-PP2Ac / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coiled-coil domain-containing protein 6

MacromoleculeName: Coiled-coil domain-containing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.322977 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGEN LYFQGSMADS ASESDTDGAG GNSSSSAAMQ SSCSSTSGGG GGGGGGGGGG KSGGIVISPF RLEELTNRLA SLQQENKVL KIELETYKLK CKALQEENRD LRKASVTIQA RAEQEEEFIS NTLFKKIQAL QKEKETLAVN YEKEEEFLTN E LSRKLMQL ...String:
MHHHHHHGEN LYFQGSMADS ASESDTDGAG GNSSSSAAMQ SSCSSTSGGG GGGGGGGGGG KSGGIVISPF RLEELTNRLA SLQQENKVL KIELETYKLK CKALQEENRD LRKASVTIQA RAEQEEEFIS NTLFKKIQAL QKEKETLAVN YEKEEEFLTN E LSRKLMQL QHEKAELEQH LEQEQEFQVN KLMKKIKKLE NDTISKQLTL EQLRREKIDL ENTLEQEQEA LVNRLWKRMD KL EAEKRIL QEKLDQPVSA PPSPRDISME IDSPENMMRH IRFLKNEVER LKKQLRAAQL QHSEKMAQYL EEERHMREEN LRL QRKLQR EMERREALCR QLSESESSLE MDDERYFNEM SAQGLRPRTV SSPIPYTPSP SSSRPISPGL SYASHTVGFT PPTS LTRAG MSYYNSPGLH VQHMGTSHGI TRPSPRRSNS PDKFKRPTPP PSPNTQTPVQ PPPPPPPPPM QPTVPSAATS QPTPS QHSA HPSSQP

UniProtKB: Coiled-coil domain-containing protein 6

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Macromolecule #2: F-box only protein 42

MacromoleculeName: F-box only protein 42 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.126867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDDDDKG ENLYFQGSRS MSELPEEVLE YILSFLSPYQ EHKTAALVCK QWYRLIKGVA HQCYHGFMKA VQEGNIQWES RTYPYPGTP ITQRFSHSAC YYDANQSMYV FGGCTQSSCN AAFNDLWRLD LNSKEWIRPL ASGSYPSPKA GATLVVYKDL L VLFGGWTR ...String:
MDYKDDDDKG ENLYFQGSRS MSELPEEVLE YILSFLSPYQ EHKTAALVCK QWYRLIKGVA HQCYHGFMKA VQEGNIQWES RTYPYPGTP ITQRFSHSAC YYDANQSMYV FGGCTQSSCN AAFNDLWRLD LNSKEWIRPL ASGSYPSPKA GATLVVYKDL L VLFGGWTR PSPYPLHQPE RFFDEIHTYS PSKNWWNCIV TTHGPPPMAG HSSCVIDDKM IVFGGSLGSR QMSNDVWVLD LE QWAWSKP NISGPSPHPR GGQSQIVIDD ATILILGGCG GPNALFKDAW LLHMHSGPWA WQPLKVENEE HGAPELWCHP ACR VGQCVV VFSQAPSGRA PLSPSLNSRP SPISATPPAL VPETREYRSQ SPVRSMDEAP CVNGRWGTLR PRAQRQTPSG SREG SLSPA RGDGSPILNG GSLSPGTAAV GGSSLDSPVQ AISPSTPSAP EGYDLKIGLS LAPRRGSLPD QKDLRLGSID LNWDL KPAS SSNPMDGMDN RTVGGSMRHP PEQTNGVHTP PHVASALAGA VSPGALRRSL EAIKAMSSKG PSASAALSPP LGSSPG SPG SQSLSSGETV PIPRPGPAQG DGHSLPPIAR RLGHHPPQSL NVGKPLYQSM NCKPMQMYVL DIKDTKEKGR VKWKVFN SS SVVGPPETSL HTVVQGRGEL IIFGGLMDKK QNVKYYPKTN ALYFVRAKR

UniProtKB: F-box only protein 42

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Macromolecule #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...

MacromoleculeName: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.858492 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDDDDKG ENLYFQGSYP YDVPDYAMDE KVFTKELDQW IEQLNECKQL SESQVKSLCE KAKEILTKES NVQEVRCPVT VCGDVHGQF HDLMELFRIG GKSPDTNYLF MGDYVDRGYY SVETVTLLVA LKVRYRERIT ILRGNHESRQ ITQVYGFYDE C LRKYGNAN ...String:
MDYKDDDDKG ENLYFQGSYP YDVPDYAMDE KVFTKELDQW IEQLNECKQL SESQVKSLCE KAKEILTKES NVQEVRCPVT VCGDVHGQF HDLMELFRIG GKSPDTNYLF MGDYVDRGYY SVETVTLLVA LKVRYRERIT ILRGNHESRQ ITQVYGFYDE C LRKYGNAN VWKYFTDLFD YLPLTALVDG QIFCLHGGLS PSIDTLDHIR ALDRLQEVPH EGPMCDLLWS DPDDRGGWGI SP RGAGYTF GQDISETFNH ANGLTLVSRA HQLVMEGYNW CHDRNVVTIF SAPNYCYRCG NQAAIMELDD TLKYSFLQFD PAP RRGEPH VTRRTPDYF(MLL)

UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

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Macromolecule #4: SKP1

MacromoleculeName: SKP1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.997295 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MGSPSIKLQS SDGEIFEVDV EIAKQSVTIK TMLEDLGMDP VPLPNVNAAI LKKVIQWCTH HKDDPGGSGT DDIPVWDQEF LKVDQGTLF ELILAANYLD IKGLLDVTCK TVANMIKGKT PEEIRKTFNI KNDFTEEEEA QVRKENQWCE EK

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Macromolecule #5: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 5 / Number of copies: 16 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES pH 7.5, 200 mM NaCl, 1 mM TCEP pH 7.5
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 2.5 / Details: coated with self assembled monolayers
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21534 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2 / Details: 15.8 eps collected as 40 frame movies
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7261626
Details: template picked from 2D classes in Glacios screening dataset
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio starting model generation from dataset
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 155244
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: NU-refinement in cryoSPARC
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC / Details: heterogeneous classification in cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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