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- EMDB-73099: Structure of AGO2 primary RISC (pri-RISC) -

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Basic information

Entry
Database: EMDB / ID: EMD-73099
TitleStructure of AGO2 primary RISC (pri-RISC)
Map data
Sample
  • Complex: Human Argonaute2 in complex with miR-20a duplex
    • Protein or peptide: Protein argonaute-2
    • RNA: 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*AP*G)-3')
    • RNA: RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*U)-3')
KeywordsArgonaute / pri-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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsZhang H / Adhav VA / Kehling AC / Nakanishi K
Funding support United States, 2 items
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 primary RISC (pri-RISC)
Authors: Zhang H / Adhav VA / Kehling AC / Nakanishi K
History
DepositionOct 9, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73099.png

Downloads & links

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Map

FileDownload / File: emd_73099.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.43 Å/pix.
x 512 pix.
= 218.112 Å		0.43 Å/pix.
x 512 pix.
= 218.112 Å		0.43 Å/pix.
x 512 pix.
= 218.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.426 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.09476841 - 0.11740281
Average (Standard dev.)-0.000023819566 (±0.00230191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 218.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73099_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73099_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 : Human Argonaute2 in complex with miR-20a duplex

EntireName: Human Argonaute2 in complex with miR-20a duplex
Components
  • Complex: Human Argonaute2 in complex with miR-20a duplex
    • Protein or peptide: Protein argonaute-2
    • RNA: 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*AP*G)-3')
    • RNA: RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*U)-3')

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Supramolecule #1: Human Argonaute2 in complex with miR-20a duplex

SupramoleculeName: Human Argonaute2 in complex with miR-20a duplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Protein argonaute-2

MacromoleculeName: Protein argonaute-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.753625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMYSGA GPALAPPAPP PPIQGYAFKP PPRPDFGTSG RTIKLQANFF EMDIPKIDIY HYELDIKPEK CPRRVNREIV EHMVQHFKT QIFGDRKPVF DGRKNLYTAM PLPIGRDKVE LEVTLPGEGK DRIFKVSIKW VSCVSLQALH DALSGRLPSV P FETIQALD ...String:
GAMGSMYSGA GPALAPPAPP PPIQGYAFKP PPRPDFGTSG RTIKLQANFF EMDIPKIDIY HYELDIKPEK CPRRVNREIV EHMVQHFKT QIFGDRKPVF DGRKNLYTAM PLPIGRDKVE LEVTLPGEGK DRIFKVSIKW VSCVSLQALH DALSGRLPSV P FETIQALD VVMRHLPSMR YTPVGRSFFT ASEGCSNPLG GGREVWFGFH QSVRPSLWKM MLNIDVSATA FYKAQPVIEF VC EVLDFKS IEEQQKPLTD SQRVKFTKEI KGLKVEITHC GQMKRKYRVC NVTRRPASHQ TFPLQQESGQ TVECTVAQYF KDR HKLVLR YPHLPCLQVG QEQKHTYLPL EVCNIVAGQR CIKKLTDNQT STMIRATARS APDRQEEISK LMRSASFNTD PYVR EFGIM VKDEMTDVTG RVLQPPSILY GGRNKAIATP VQGVWDMRNK QFHTGIEIKV WAIACFAPQR QCTEVHLKSF TEQLR KISR DAGMPIQGQP CFCKYAQGAD SVEPMFRHLK NTYAGLQLVV VILPGKTPVY AEVKRVGDTV LGMATQCVQM KNVQRT TPQ TLSNLCLKIN VKLGGVNNIL LPQGRPPVFQ QPVIFLGADV THPPAGDGKK PSIAAVVGSM DAHPNRYCAT VRVQQHR QE IIQDLAAMVR ELLIQFYKST RFKPTRIIFY RDGVSEGQFQ QVLHHELLAI REACIKLEKD YQPGITFIVV QKRHHTRL F CTDKNERVGK SGNIPAGTTV DTKITHPTEF DFYLCSHAGI QGTSRPSHYH VLWDDNRFSS DELQILTYQL CHTYVRCTR SVSIPAPAYY AHLVAFRARY HLVDKEHDSA EGSHTSGQSN GRDHQALAKA VQVHQDTLRT MYFA

UniProtKB: Protein argonaute-2

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Macromolecule #2: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*AP...

MacromoleculeName: 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*AP*G)-3')
type: rna / ID: 2 / Details: miR-20a / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.429449 KDa
SequenceString:
UAAAGUGCUU AUAGUGCAGG UAG

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Macromolecule #3: RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*AP*CP*CP*UP*GP*CP*AP*CP*UP*AP*UP*AP*AP*GP*CP*AP*CP*U)-3')
type: rna / ID: 3 / Details: modified miR-20a passenger / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.970421 KDa
SequenceString:
AAGAGACCUG CACUAUAAGC ACUUUAAG

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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

Concentration0.38 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 2 mM bis(sulfosuccinimidyl)suberate
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10091 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 0.01 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4) / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 203008
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9ym9:
Structure of AGO2 primary RISC (pri-RISC)

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