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- EMDB-75677: Human Argonaute2 WT - guide(3 prime-amino) RNA in complex with a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75677
TitleHuman Argonaute2 WT - guide(3 prime-amino) RNA in complex with a fully complementary target
Map data
Sample
  • Complex: human Argonaute-2 - miR-122(3'-amino) in complex with a fully complementary target
    • Protein or peptide: Argonaute2 WT
    • RNA: guide(3 prime-amino) RNA
    • RNA: target RNA
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRNA binding protein / RNP / RNA / Argonaute2 / Ago2 / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSarkar S / Gebert LFR / MacRae IJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM127090 United States
CitationJournal: To Be Published
Title: Human Argonaute2 WT - miR-122(3'-amino) in complex with a fully complementary target
Authors: Sarkar S / Gebert LFR / MacRae IJ
History
DepositionFeb 23, 2026-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75677.png

Downloads & links

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Map

FileDownload / File: emd_75677.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.90143746 - 1.5089965
Average (Standard dev.)-0.000023281353 (±0.03440093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 222.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75677_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_75677_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 - miR-122(3'-amino) in complex with a fully com...

EntireName: human Argonaute-2 - miR-122(3'-amino) in complex with a fully complementary target
Components
  • Complex: human Argonaute-2 - miR-122(3'-amino) in complex with a fully complementary target
    • Protein or peptide: Argonaute2 WT
    • RNA: guide(3 prime-amino) RNA
    • RNA: target RNA
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: human Argonaute-2 - miR-122(3'-amino) in complex with a fully com...

SupramoleculeName: human Argonaute-2 - miR-122(3'-amino) in complex with a fully complementary target
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Argonaute2 WT

MacromoleculeName: Argonaute2 WT / 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: 97.402195 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYSGAGPALA PPAPPPPIQG YAFKPPPRPD FGTSGRTIKL QANFFEMDIP KIDIYHYELD IKPEKCPRRV NREIVEHMVQ HFKTQIFGD RKPVFDGRKN LYTAMPLPIG RDKVELEVTL PGEGKDRIFK VSIKWVSCVS LQALHDALSG RLPSVPFETI Q ALDVVMRH ...String:
MYSGAGPALA PPAPPPPIQG YAFKPPPRPD FGTSGRTIKL QANFFEMDIP KIDIYHYELD IKPEKCPRRV NREIVEHMVQ HFKTQIFGD RKPVFDGRKN LYTAMPLPIG RDKVELEVTL PGEGKDRIFK VSIKWVSCVS LQALHDALSG RLPSVPFETI Q ALDVVMRH LPSMRYTPVG RSFFTASEGC SNPLGGGREV WFGFHQSVRP SLWKMMLNID VSATAFYKAQ PVIEFVCEVL DF KSIEEQQ KPLTDSQRVK FTKEIKGLKV EITHCGQMKR KYRVCNVTRR PASHQTFPLQ QESGQTVECT VAQYFKDRHK LVL RYPHLP CLQVGQEQKH TYLPLEVCNI VAGQRCIKKL TDNQTSTMIR ATARSAPDRQ EEISKLMRSA DFNTDPYVRE FGIM VKDEM TDVTGRVLQP PSILYGGRNK AIATPVQGVW DMRNKQFHTG IEIKVWAIAC FAPQRQCTEV HLKSFTEQLR KISRD AGMP IQGQPCFCKY AQGADSVEPM FRHLKNTYAG LQLVVVILPG KTPVYAEVKR VGDTVLGMAT QCVQMKNVQR TTPQTL SNL CLKINVKLGG VNNILLPQGR PPVFQQPVIF LGADVTHPPA GDGKKPSIAA VVGSMDAHPN RYCATVRVQQ HRQEIIQ DL AAMVRELLIQ FYKSTRFKPT RIIFYRDGVS EGQFQQVLHH ELLAIREACI KLEKDYQPGI TFIVVQKRHH TRLFCTDK N ERVGKSGNIP AGTTVDTKIT HPTEFDFYLC SHAGIQGTSR PSHYHVLWDD NRFSSDELQI LTYQLCHTYV RCTRSVSIP APAYYAHLVA FRARYHLVDK EHDAAEGDHT DGQANGRDHQ ALAKAVQVHQ DTLRTMYFA

UniProtKB: Protein argonaute-2

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Macromolecule #2: guide(3 prime-amino) RNA

MacromoleculeName: guide(3 prime-amino) RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.481856 KDa
SequenceString:
UGGAGUGUGA CAAUGGUGUU

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Macromolecule #3: target RNA

MacromoleculeName: target RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.258423 KDa
SequenceString:
AAACACCAUU GUCACACUCC AAA

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTRISTRIS
100.0 mMNaClNaCl
0.5 mMTCEPTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 6 / Number real images: 20132 / Average exposure time: 3.2 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 207140
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.7)

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Atomic model buiding 1

Initial modelPDB ID:

6n4o


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-11gi:
Human Argonaute2 WT - guide(3 prime-amino) RNA in complex with a fully complementary target

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