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- EMDB-54349: Map B Locally refined interactions of ZSWIM8-CUL3 complex bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-54349
TitleMap B Locally refined interactions of ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
Map dataSharpened map of focus refined interactions of trigger-AGO with ZSWIM8.
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: Nature / Year: 2026
Title: The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation.
Authors: Jakob Farnung / Elena Slobodyanyuk / Peter Y Wang / Lianne W Blodgett / Daniel H Lin / Susanne von Gronau / Brenda A Schulman / David P Bartel /
Abstract: MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including messenger RNAs from most human genes. Within each complex, the miRNA pairs to ...MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including messenger RNAs from most human genes. Within each complex, the miRNA pairs to target RNAs, and AGO provides effector function while also protecting the miRNA from cellular nucleases. Although much is known about miRNA-directed gene regulation, less is known about how miRNAs themselves are regulated. One pathway that regulates miRNAs involves unusual targets called 'trigger' RNAs, which reverse the canonical regulatory logic and instead down-regulate miRNAs. This target-directed miRNA degradation (TDMD) is thought to require a cullin-RING E3 ligase because it depends on the cullin protein CUL3 and other ubiquitylation components, including the BC-box protein ZSWIM8 (refs. ). ZSWIM8 is required for murine perinatal viability and for destabilization of most short-lived miRNAs, which suggests biological importance of TDMD. Here, biochemical and cellular assays establish AGO binding and polyubiquitylation by the ZSWIM8-CUL3 E3 ligase as the key regulatory steps of TDMD, and thereby define a unique cullin-RING E3 ligase class. Cryogenic electron microscopy analyses show ZSWIM8 recognizing distinct AGO and RNA conformations shaped by pairing of the miRNA to the trigger. Specificity of AGO ubiquitylation is established through generalizable RNA-RNA, RNA-protein and protein-protein interactions. The substrate features recognized by the E3 ligase do not conform to a conventional degron but instead establish a two-RNA-factor authentication mechanism for specifying a protein ubiquitylation substrate.
History
DepositionJul 10, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54349.png

Downloads & links

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Map

FileDownload / File: emd_54349.map.gz / Format: CCP4 / Size: 891.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of focus refined interactions of trigger-AGO with ZSWIM8.
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: 0.0854
Minimum - Maximum-0.44522452 - 0.89123863
Average (Standard dev.)-0.000057880872 (±0.010977069)
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_54349_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: DeepEMhancer sharpened map of focus refined interactions of...

Fileemd_54349_additional_1.map
AnnotationDeepEMhancer sharpened map of focus refined interactions of trigger-AGO with ZSWIM8.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54349_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54349_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 : 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 / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2.) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Screening dataset derived map was used as an initial model.
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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