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- PDB-9rwz: ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO -

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Basic information

Entry
Database: PDB / ID: 9rwz
TitleZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
Components
  • CYRANO trigger RNA
  • Cullin-3
  • Elongin-B
  • Elongin-C
  • Protein argonaute-2
  • Zinc finger SWIM domain-containing protein 8
  • miR-7
KeywordsLIGASE / miRNA / E3 Ligase
Function / homology
Function and homology information


positive regulation of miRNA catabolic process / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / POZ domain binding / miRNA-mediated gene silencing by mRNA destabilization ...positive regulation of miRNA catabolic process / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / POZ domain binding / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / RNA stabilization / Small interfering RNA (siRNA) biogenesis / Regulation of CDH1 mRNA translation by microRNAs / positive regulation of trophoblast cell migration / polar microtubule / Transcriptional Regulation by MECP2 / nuclear protein quality control by the ubiquitin-proteasome system / COPII vesicle coating / regulation protein catabolic process at postsynapse / anaphase-promoting complex-dependent catabolic process / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / RHOBTB3 ATPase cycle / embryonic cleavage / RNA 7-methylguanosine cap binding / pre-miRNA processing / regulation of synapse maturation / siRNA processing / siRNA binding / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / target-directed miRNA degradation / positive regulation of mitotic metaphase/anaphase transition / RISC complex / elongin complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / Notch binding / fibroblast apoptotic process / cell projection organization / Regulation of RUNX1 Expression and Activity / P-body assembly / negative regulation of Rho protein signal transduction / RHOBTB1 GTPase cycle / miRNA binding / VCB complex / MicroRNA (miRNA) biogenesis / Cul5-RING ubiquitin ligase complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / stem cell division / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / mitotic metaphase chromosome alignment / negative regulation of type I interferon production / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of cytokinesis / ubiquitin ligase complex scaffold activity / RNA polymerase II complex binding / protein quality control for misfolded or incompletely synthesized proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Regulation of MECP2 expression and activity / endoplasmic reticulum to Golgi vesicle-mediated transport / protein monoubiquitination / RHOBTB2 GTPase cycle / sperm flagellum / Tat-mediated elongation of the HIV-1 transcript / core promoter sequence-specific DNA binding / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein autoubiquitination / protein K48-linked ubiquitination / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / ubiquitin-like ligase-substrate adaptor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Nuclear events stimulated by ALK signaling in cancer / RNA endonuclease activity / translation initiation factor activity / gastrulation / regulation of cellular response to insulin stimulus / RNA Polymerase II Pre-transcription Events / negative regulation of translational initiation / positive regulation of TORC1 signaling
Similarity search - Function
: / : / ZSWIM4-8, C-terminal / ZSWIM8, TPR repeats / Zinc finger, SWIM-type / Zinc finger SWIM-type profile. / Protein argonaute-2 / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain ...: / : / ZSWIM4-8, C-terminal / ZSWIM8, TPR repeats / Zinc finger, SWIM-type / Zinc finger SWIM-type profile. / Protein argonaute-2 / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / : / Cullin alpha+beta domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / PAZ domain profile. / Cullin protein neddylation domain / PAZ domain / Cullin, N-terminal / Elongin-C / Elongin B / Cullin alpha solenoid domain / Cullin / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Zinc finger SWIM domain-containing protein 8 / Cullin-3 / Elongin-C / Elongin-B / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFarnung, J. / Slobodyanyuk, E. / Bartel, D.P. / Schulman, B.A.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101098161European Union
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: E3 ligase mechanism of target-directed microRNA degradation
Authors: Farnung, J. / Slobodyanyuk, E. / Wang, P.Y. / Lin, D.H. / Blodgett, L.A. / Schulman, B.A. / Bartel, D.P.
History
DepositionJul 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute-2
B: Elongin-B
C: Elongin-B
D: Elongin-C
E: Elongin-C
G: miR-7
H: Cullin-3
I: Cullin-3
T: CYRANO trigger RNA
N: Zinc finger SWIM domain-containing protein 8
M: Zinc finger SWIM domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)689,95613
Polymers689,82511
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules ABCDEHINM

#1: Protein Protein argonaute-2 / Argonaute2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation ...Argonaute2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF-2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 98554.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine purification tag was not removed.
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q15370
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 12485.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q15369
#5: Protein Cullin-3 / CUL-3


Mass: 46410.113 Da / Num. of mol.: 2 / Mutation: I342R, L346D
Source method: isolated from a genetically manipulated source
Details: CUL3 NTD containing solubilizing mutations I342R, L346D, and remnant of C-terminal TEV protease cleavage site.
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13618
#7: Protein Zinc finger SWIM domain-containing protein 8


Mass: 200458.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal twin-strep purification tag was not removed.
Source: (gene. exp.) Homo sapiens (human) / Gene: ZSWIM8, KIAA0913 / Production host: Spodoptera (butterflies/moths) / References: UniProt: A7E2V4

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RNA chain , 2 types, 2 molecules GT

#4: RNA chain miR-7


Mass: 7690.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' terminus is phosphorylated / Source: (synth.) Homo sapiens (human)
#6: RNA chain CYRANO trigger RNA


Mass: 38577.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 2994212338

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Non-polymers , 1 types, 2 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
Type: COMPLEX
Details: Complex formed of CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 7.8 / Details: 25 mM HEPES, 50 mM NaCl, 1 mM TCEP, pH 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
9PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230859 / Symmetry type: POINT

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