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- EMDB-54348: Map A ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO -

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Basic information

Entry
Database: EMDB / ID: EMD-54348
TitleMap A ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
Map dataConsensus map.
Sample
  • Complex: CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3
KeywordsmiRNA / E3 ligase / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFarnung J / Slobodyanyuk E / Bartel DP / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101098161European Union
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation
Authors: Farnung J / Slobodyanyuk E / Wang PY / Lin DH / Blodgett LA / Schulman BA / Bartel DP
History
DepositionJul 10, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54348.png

Downloads & links

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Map

FileDownload / File: emd_54348.map.gz / Format: CCP4 / Size: 891.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 616 pix.
= 524.339 Å		0.85 Å/pix.
x 616 pix.
= 524.339 Å		0.85 Å/pix.
x 616 pix.
= 524.339 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0796
Minimum - Maximum-0.39046666 - 0.7289229
Average (Standard dev.)0.000026202748 (±0.008015312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions616616616
Spacing616616616
CellA=B=C: 524.3392 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54348_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 10 Angstrom low-pass filtered Consensus Map.

Fileemd_54348_additional_1.map
Annotation10 Angstrom low-pass filtered Consensus Map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened Consensus Map.

Fileemd_54348_additional_2.map
AnnotationUnsharpened Consensus Map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of consensus map.

Fileemd_54348_half_map_1.map
AnnotationHalf map of consensus map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of consensus map.

Fileemd_54348_half_map_2.map
AnnotationHalf map of consensus 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 : CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3

EntireName: CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3
Components
  • Complex: CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3

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Supramolecule #1: CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3

SupramoleculeName: CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3
type: complex / ID: 1 / Parent: 0
Details: Complex formed of CYRANO-AGO2-miR-7 in complex with ZSWIM8 ELONGIN B/C, CUL3
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: 7.8 / Details: 25 mM HEPES, 50 mM NaCl, 1 mM TCEP, pH 7.8
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234181
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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