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- EMDB-49977: Focused refinement of PP2Ac repeats 2 and 3 of the FBXO42-CCDC6-P... -

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Basic information

Entry
Database: EMDB / ID: EMD-49977
TitleFocused refinement of PP2Ac repeats 2 and 3 of the FBXO42-CCDC6-PP2Ac degradasome
Map data
Sample
  • Complex: Complex of FBXO42-CCDC6-PP2Ac
KeywordsE3 ligase / phosphatase / scaffolding / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHsu PL / Michaelian N / Azumaya C / Coassolo S / Yauch RL
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: The SCFFBXO42-CCDC6 axis regulates proteosomal degradation of the catalytic subunit of PP2A
Authors: Hsu PL / Michaelian N / Azumaya C / Coassolo S / Yauch RL / Maculins T / Dimitrova Y
History
DepositionApr 2, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49977.png

Downloads & links

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Map

FileDownload / File: emd_49977.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.838 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10018152 - 0.236004
Average (Standard dev.)-0.00009862711 (±0.004266129)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_49977_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_49977_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49977_half_map_2.map
Projections & Slices
AxesZYX

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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

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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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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: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 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

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