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- EMDB-55558: The Cullin 2 RING VHL E3 ligase dimerized by the homoPROTAC CM11,... -

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Basic information

Entry
Database: EMDB / ID: EMD-55558
TitleThe Cullin 2 RING VHL E3 ligase dimerized by the homoPROTAC CM11, C1 symmetry
Map data
Sample
  • Complex: The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11
KeywordsPROTAC / homoPROTAC / stabiliser / VHL / von Hippel-Lindau / Cullin / RING. ubiquitination / degradation / TPD / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsCrowe C / Ciulli A
Funding supportEuropean Union, United Kingdom, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2012-StG-311460 DrugE3CRLsEuropean Union
European Research Council (ERC)875510European Union
Medical Research Council (MRC, United Kingdom)MR/R015791/1 United Kingdom
Wellcome Trust223816/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)PO 4050845509 United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Linker-rigidified VHL homodimerizers convert degraders into stabilizers of non-ubiquitinable ternary complexes
Authors: Crowe C / Salerno A / Sathe G / Marsh G / Maple H / Ciulli A
History
DepositionNov 3, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55558.png

Downloads & links

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Map

FileDownload / File: emd_55558.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 600 pix.
= 444. Å		0.74 Å/pix.
x 600 pix.
= 444. Å		0.74 Å/pix.
x 600 pix.
= 444. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0376
Minimum - Maximum-0.051120635 - 0.16672507
Average (Standard dev.)0.00048738837 (±0.0037581236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55558_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55558_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11

EntireName: The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11
Components
  • Complex: The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11

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Supramolecule #1: The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11

SupramoleculeName: The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11
type: complex / ID: 1 / 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 state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.7 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49680
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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