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- EMDB-76216: Structure of AGO2 RISC with a 16-nt target -

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Basic information

Entry
Database: EMDB / ID: EMD-76216
TitleStructure of AGO2 RISC with a 16-nt target
Map data
Sample
  • Complex: Human Argonaute 2 in complex with a guide and a target
    • RNA: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*A)-3')
    • RNA: RNA (5'-R(P*CP*AP*CP*UP*AP*(OMU)P*(SRA)P*AP*GP*CP*AP*CP*U)-3')
    • Protein or peptide: Protein argonaute-2
KeywordsArgonaute2 / RNAi / target / 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 / Small interfering RNA (siRNA) biogenesis / Regulation of CDH1 mRNA translation by microRNAs / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / Regulation of PD-L1(CD274) translation / RISC-loading complex / mRNA cap binding / miRNA processing / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / pre-miRNA processing / regulation of synapse maturation / 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 / positive regulation of translation / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / P-body / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / postsynapse / single-stranded RNA binding / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
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: 3.29 Å
AuthorsZhang H / Nakanishi K
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124320 United States
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)R35GM161485 United States
CitationJournal: To Be Published
Title: Structure of AGO2 RISC with an 18-nt target
Authors: Zhang H / Nakanishi K
History
DepositionMar 19, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76216.png

Downloads & links

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Map

FileDownload / File: emd_76216.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 218.112 Å		0.85 Å/pix.
x 256 pix.
= 218.112 Å		0.85 Å/pix.
x 256 pix.
= 218.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.7395398 - 0.9822172
Average (Standard dev.)0.00039696405 (±0.019880285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
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_76216_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_76216_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 Argonaute 2 in complex with a guide and a target

EntireName: Human Argonaute 2 in complex with a guide and a target
Components
  • Complex: Human Argonaute 2 in complex with a guide and a target
    • RNA: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*A)-3')
    • RNA: RNA (5'-R(P*CP*AP*CP*UP*AP*(OMU)P*(SRA)P*AP*GP*CP*AP*CP*U)-3')
    • Protein or peptide: Protein argonaute-2

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Supramolecule #1: Human Argonaute 2 in complex with a guide and a target

SupramoleculeName: Human Argonaute 2 in complex with a guide and a target
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human Argonaute 2 in complex with 23-nt miR-20a and an 18 nt fully-complementary target
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 KDa

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

MacromoleculeName: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*GP*CP*A)-3')
type: rna / ID: 1 / Details: miR-20a guide / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.429449 KDa
SequenceString:
UAAAGUGCUU AUAGUGCAGG UAG

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Macromolecule #2: RNA (5'-R(P*CP*AP*CP*UP*AP*(OMU)P*(SRA)P*AP*GP*CP*AP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*CP*AP*CP*UP*AP*(OMU)P*(SRA)P*AP*GP*CP*AP*CP*U)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.715545 KDa
SequenceString:
CACUA(OMU)(SRA)AGC ACUUUAAA

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Macromolecule #3: Protein argonaute-2

MacromoleculeName: Protein argonaute-2 / type: protein_or_peptide / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.36 mg/mL
BufferpH: 7.5
Details: 50 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2, 0.5 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: 4152 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / 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 correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.21-5207-000) / Number images used: 61071
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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