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- PDB-9yma: Structure of AGO2 vise-RISC -

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Basic information

Entry
Database: PDB / ID: 9yma
TitleStructure of AGO2 vise-RISC
Components
  • Protein argonaute-2
  • RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*AP*GP*GP*UP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / Argonaute / wedg1-RISC / RNAi / RISC assembly / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-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 / miRNA-mediated gene silencing by mRNA destabilization ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-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 / miRNA-mediated gene silencing by mRNA destabilization / negative regulation of amyloid precursor protein biosynthetic process / RNA stabilization / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Regulation of CDH1 mRNA translation by microRNAs / Transcriptional Regulation by MECP2 / 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 / 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 / RISC complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / Regulation of RUNX1 Expression and Activity / P-body assembly / miRNA binding / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / core promoter sequence-specific DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Nuclear events stimulated by ALK signaling in cancer / RNA endonuclease activity / translation initiation factor activity / negative regulation of translational initiation / post-embryonic development / TP53 Regulates Metabolic Genes / positive regulation of translation / P-body / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / positive regulation of angiogenesis / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / postsynapse / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 / PAZ domain profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsZhang, H. / Adhav, V.A. / Kehling, A.C. / Nakanishi, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124320 United States
CitationJournal: To Be Published
Title: Structure of AGO2 vise-RISC
Authors: Zhang, H. / Adhav, V.A. / Kehling, A.C. / Nakanishi, K.
History
DepositionOct 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 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
B: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*AP*GP*GP*UP*A)-3')
C: RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*UP*UP*U)-3')
A: Protein argonaute-2


Theoretical massNumber of molelcules
Total (without water)114,1533
Polymers114,1533
Non-polymers00
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

#1: RNA chain RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*AP*GP*GP*UP*A)-3')


Mass: 7429.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: miR-20a / Source: (synth.) Homo sapiens (human)
#2: RNA chain RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*UP*UP*U)-3')


Mass: 8970.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: modified miR-20a passenger / Source: (synth.) Homo sapiens (human)
#3: 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: 97753.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
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: Human Argonaute 2 in complex with an RNA duplex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Details: 20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 2 mM bis(sulfosuccinimidyl)suberate.
SpecimenConc.: 0.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10091

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2EPUimage acquisition
4cryoSPARCv4CTF correction
7UCSF ChimeraX1-6.1model fitting
8Coot0.9.8.91model fitting
13cryoSPARC3D reconstruction
20PHENIX1.21.2_5419model refinement
21UCSF ChimeraX1-6.1model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64361 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDSource nameTypeAccession code
11AlphaFoldin silico model
24W5N

4w5n

1PDBexperimental model4W5N
RefinementHighest resolution: 3.87 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036287
ELECTRON MICROSCOPYf_angle_d0.538711
ELECTRON MICROSCOPYf_dihedral_angle_d16.9082581
ELECTRON MICROSCOPYf_chiral_restr0.0391000
ELECTRON MICROSCOPYf_plane_restr0.004974

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