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- EMDB-72968: 6.9 A map of 3 x FBXO42-SKP1 bound to CCDC6-PP2Ac -

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Basic information

Entry
Database: EMDB / ID: EMD-72968
Title6.9 A map of 3 x FBXO42-SKP1 bound to CCDC6-PP2Ac
Map dataFBXO42-SKP1 bound to CCDC6-PP2Ac
Sample
  • Complex: Complex of CCDC6-mPP2Ac bound by 3 copies of FBXO42-SKP1
KeywordsUbiquitin ligase / E3 / phosphatase / coiled-coil / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsMichaelian N / Azumaya CM / Hsu PL
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
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
DepositionSep 30, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72968.png

Downloads & links

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Map

FileDownload / File: emd_72968.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFBXO42-SKP1 bound to CCDC6-PP2Ac
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.15 Å/pix.
x 256 pix.
= 549.606 Å		2.15 Å/pix.
x 256 pix.
= 549.606 Å		2.15 Å/pix.
x 256 pix.
= 549.606 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1469 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.41720864 - 0.98046476
Average (Standard dev.)-0.00027397994 (±0.02860222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 549.6064 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap A

Fileemd_72968_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_72968_half_map_2.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of CCDC6-mPP2Ac bound by 3 copies of FBXO42-SKP1

EntireName: Complex of CCDC6-mPP2Ac bound by 3 copies of FBXO42-SKP1
Components
  • Complex: Complex of CCDC6-mPP2Ac bound by 3 copies of FBXO42-SKP1

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Supramolecule #1: Complex of CCDC6-mPP2Ac bound by 3 copies of FBXO42-SKP1

SupramoleculeName: Complex of CCDC6-mPP2Ac bound by 3 copies of FBXO42-SKP1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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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 / Details: 20 mM HEPES pH 7.5, 200 mM NaCl, 1 mM TCEP pH 7.5
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 25
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 44833 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 30.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2468634
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: ab initio in cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28195
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC

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