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- EMDB-16588: CAND1-SCF-FBXO6 CAND1 engaged SCF rocked -

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Basic information

Entry
Database: EMDB / ID: EMD-16588
TitleCAND1-SCF-FBXO6 CAND1 engaged SCF rocked
Map dataRelion Postprocess
Sample
  • Complex: CAND1-SCF-FBXO6 CAND1 engaged SCF rocked
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.54 Å
AuthorsBaek K / Schulman BA
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)789016European Union
CitationJournal: Cell / Year: 2023
Title: Systemwide disassembly and assembly of SCF ubiquitin ligase complexes.
Authors: Kheewoong Baek / Daniel C Scott / Lukas T Henneberg / Moeko T King / Matthias Mann / Brenda A Schulman /
Abstract: Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much ...Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much protein degradation, require CAND1 to distribute the limiting CUL1 subunit across the family of ∼70 different F box proteins. Yet, how a single factor coordinately assembles numerous distinct multiprotein complexes remains unknown. We obtained cryo-EM structures of CAND1-bound SCF complexes in multiple states and correlated mutational effects on structures, biochemistry, and cellular assays. The data suggest that CAND1 clasps idling catalytic domains of an inactive SCF, rolls around, and allosterically rocks and destabilizes the SCF. New SCF production proceeds in reverse, through SKP1-F box allosterically destabilizing CAND1. The CAND1-SCF conformational ensemble recycles CUL1 from inactive complexes, fueling mixing and matching of SCF parts for E3 activation in response to substrate availability. Our data reveal biogenesis of a predominant family of E3 ligases, and the molecular basis for systemwide multiprotein complex assembly.
History
DepositionJan 31, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16588.png

Downloads & links

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Map

FileDownload / File: emd_16588.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion Postprocess
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 160 pix.
= 301.6 Å		1.89 Å/pix.
x 160 pix.
= 301.6 Å		1.89 Å/pix.
x 160 pix.
= 301.6 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.036572102 - 0.113546394
Average (Standard dev.)4.4804226e-05 (±0.0063934466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 301.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16588_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: 3D Refinement

Fileemd_16588_additional_1.map
Annotation3D Refinement
Projections & Slices
AxesZYX

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Half map: halfmap1

Fileemd_16588_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2

Fileemd_16588_half_map_2.map
Annotationhalfmap2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : CAND1-SCF-FBXO6 CAND1 engaged SCF rocked

EntireName: CAND1-SCF-FBXO6 CAND1 engaged SCF rocked
Components
  • Complex: CAND1-SCF-FBXO6 CAND1 engaged SCF rocked

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Supramolecule #1: CAND1-SCF-FBXO6 CAND1 engaged SCF rocked

SupramoleculeName: CAND1-SCF-FBXO6 CAND1 engaged SCF rocked / type: complex / ID: 1 / Chimera: Yes / Parent: 0
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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11468
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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