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- EMDB-55237: EloB/EloC/VHL/CV2a/14-3-3zeta/ERa pose 3 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55237
TitleEloB/EloC/VHL/CV2a/14-3-3zeta/ERa pose 3
Map data
Sample
  • Complex: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
KeywordsE3 ligase / von Hippel-Lindau / VHL / Elongin C / Elongin B / 14-3-3 / estrogen receptor alpha / PROTAC / proteolysis targeted chimera / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsCrowe C / Nakasone MA / Harzing T / Verhoef CJA / Cossar PJ / Ciulli A
Funding supportEuropean Union, United Kingdom, 3 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
CitationJournal: Biorxiv / Year: 2025
Title: Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC design
Authors: Verhoef CJA / Crowe C / Nakasone MA / DeLaCuadra-Baste A / Harzing T / Span NAS / Sathe G / Iso K / Ottmann C / Brunsveld L / Ciulli A / Cossar PJ
History
DepositionSep 30, 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_55237.png

Downloads & links

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Map

FileDownload / File: emd_55237.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.7 Å		0.83 Å/pix.
x 300 pix.
= 248.7 Å		0.83 Å/pix.
x 300 pix.
= 248.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0703
Minimum - Maximum-0.24436261 - 0.7418426
Average (Standard dev.)0.00069301995 (±0.012855657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55237_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55237_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 : Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippe...

EntireName: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
Components
  • Complex: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha

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Supramolecule #1: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippe...

SupramoleculeName: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
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 stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 99236
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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