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- EMDB-75218: Structure of Human Argonaute2-miR200b RISC bound to 14nt long tar... -

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Basic information

Entry
Database: EMDB / ID: EMD-75218
TitleStructure of Human Argonaute2-miR200b RISC bound to 14nt long target in complex with kinase CK1alpha
Map data
Sample
  • Complex: Argonaute2-miR200 bound to 14 nt target RNA and Ck1alpha kinase
    • Protein or peptide: Protein argonaute-2
    • Protein or peptide: Casein kinase I isoform alpha
    • RNA: RNA (5'-R(P*UP*AP*AP*UP*AP*CP*UP*GP*CP*CP*UP*GP*GP*UP*AP*AP*UP*GP*AP*UP*GP*A)-3')
    • RNA: RNA (5'-R(P*AP*CP*CP*UP*AP*UP*CP*AP*GP*UP*AP*UP*UP*A)-3')
KeywordsmiRNA / target / RNA binding protein / HYDROLASE-TRANSFERASE-RNA complex
Function / homology
Function and homology information


intermediate filament cytoskeleton organization / : / 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 / negative regulation of NLRP3 inflammasome complex assembly ...intermediate filament cytoskeleton organization / : / 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 / negative regulation of NLRP3 inflammasome complex assembly / 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 / Activation of SMO / Transcriptional Regulation by MECP2 / Regulation of PD-L1(CD274) translation / RISC-loading complex / cellular response to nutrient / miRNA processing / mRNA cap binding / beta-catenin destruction complex / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / miRNA-mediated gene silencing by inhibition of translation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / regulatory ncRNA-mediated gene silencing / pre-miRNA processing / RNA 7-methylguanosine cap binding / regulation of synapse maturation / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / mRNA 3'-UTR AU-rich region binding / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / TGFBR3 expression / MTOR signalling / Regulation of RUNX1 Expression and Activity / Disassembly of the destruction complex and recruitment of AXIN to the membrane / P-body assembly / miRNA binding / MicroRNA (miRNA) biogenesis / Maturation of nucleoprotein / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of Rho protein signal transduction / Wnt signaling pathway / Golgi organization / 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 / RNA endonuclease activity / Nuclear events stimulated by ALK signaling in cancer / translation initiation factor activity / negative regulation of translational initiation / positive regulation of TORC1 signaling / negative regulation of canonical Wnt signaling pathway / TP53 Regulates Metabolic Genes / positive regulation of translation / Transcriptional regulation by small RNAs / P-body / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Pre-NOTCH Transcription and Translation / spindle / positive regulation of angiogenesis / cytoplasmic ribonucleoprotein granule / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cilium / double-stranded RNA binding / ciliary basal body / Ca2+ pathway / Estrogen-dependent gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / protein kinase activity / protein phosphorylation / postsynapse / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / single-stranded RNA binding / viral protein processing / translation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome
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 / : ...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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Casein kinase I isoform alpha / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGarg A / Joshua-Tor L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structure of Human Argonaute2-miR200b RISC bound to 14nt long target in complex with kinase CK1alpha
Authors: Garg A / Joshua-Tor L
History
DepositionJan 22, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75218.png

Downloads & links

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Map

FileDownload / File: emd_75218.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 224 pix.
= 191.744 Å		0.86 Å/pix.
x 224 pix.
= 191.744 Å		0.86 Å/pix.
x 224 pix.
= 191.744 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.081
Minimum - Maximum-0.03672816 - 0.22967921
Average (Standard dev.)0.0031672232 (±0.01484873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 191.744 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_75218_additional_1.map
Projections & Slices
AxesZYX

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Additional map: DeepEMhancer modified map

Fileemd_75218_additional_2.map
AnnotationDeepEMhancer modified map
Projections & Slices
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Half map: #2

Fileemd_75218_half_map_1.map
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Half map: #1

Fileemd_75218_half_map_2.map
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Sample components

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Entire : Argonaute2-miR200 bound to 14 nt target RNA and Ck1alpha kinase

EntireName: Argonaute2-miR200 bound to 14 nt target RNA and Ck1alpha kinase
Components
  • Complex: Argonaute2-miR200 bound to 14 nt target RNA and Ck1alpha kinase
    • Protein or peptide: Protein argonaute-2
    • Protein or peptide: Casein kinase I isoform alpha
    • RNA: RNA (5'-R(P*UP*AP*AP*UP*AP*CP*UP*GP*CP*CP*UP*GP*GP*UP*AP*AP*UP*GP*AP*UP*GP*A)-3')
    • RNA: RNA (5'-R(P*AP*CP*CP*UP*AP*UP*CP*AP*GP*UP*AP*UP*UP*A)-3')

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Supramolecule #1: Argonaute2-miR200 bound to 14 nt target RNA and Ck1alpha kinase

SupramoleculeName: Argonaute2-miR200 bound to 14 nt target RNA and Ck1alpha kinase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 97.42125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AMYSGAGPAL APPAPPPPIQ GYAFKPPPRP DFGTSGRTIK LQANFFEMDI PKIDIYHYEL DIKPEKCPRR VNREIVEHMV QHFKTQIFG DRKPVFDGRK NLYTAMPLPI GRDKVELEVT LPGEGKDRIF KVSIKWVSCV SLQALHDALS GRLPSVPFET I QALDVVMR ...String:
AMYSGAGPAL APPAPPPPIQ GYAFKPPPRP DFGTSGRTIK LQANFFEMDI PKIDIYHYEL DIKPEKCPRR VNREIVEHMV QHFKTQIFG DRKPVFDGRK NLYTAMPLPI GRDKVELEVT LPGEGKDRIF KVSIKWVSCV SLQALHDALS GRLPSVPFET I QALDVVMR HLPSMRYTPV GRSFFTASEG CSNPLGGGRE VWFGFHQSVR PSLWKMMLNI DVSATAFYKA QPVIEFVCEV LD FKSIEEQ QKPLTDSQRV KFTKEIKGLK VEITHCGQMK RKYRVCNVTR RPASHQTFPL QQESGQTVEC TVAQYFKDRH KLV LRYPHL PCLQVGQEQK HTYLPLEVCN IVAGQRCIKK LTDNQTSTMI RATARSAPDR QEEISKLMRS ASFNTDPYVR EFGI MVKDE MTDVTGRVLQ PPSILYGGRN KAIATPVQGV WDMRNKQFHT GIEIKVWAIA CFAPQRQCTE VHLKSFTEQL RKISR DAGM PIQGQPCFCK YAQGADSVEP MFRHLKNTYA GLQLVVVILP GKTPVYAEVK RVGDTVLGMA TQCVQMKNVQ RTTPQT LSN LCLKINVKLG GVNNILLPQG RPPVFQQPVI FLGADVTHPP AGDGKKPSIA AVVGSMDAHP NRYCATVRVQ QHRQEII QD LAAMVRELLI QFYKSTRFKP TRIIFYRDGV SEGQFQQVLH HELLAIREAC IKLEKDYQPG ITFIVVQKRH HTRLFCTD K NERVGKSGNI PAGTTVDTKI THPTEFDFYL CSHAGIQGTS RPSHYHVLWD DNRFSSDELQ ILTYQLCHTY VRCTRSVSI PAPAYYAHLV AFRARYHLVD KEHDSAEGSH TSGQSNGRDH QALAKAVQVH QDTLRTMYFA

UniProtKB: Protein argonaute-2

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Macromolecule #2: Casein kinase I isoform alpha

MacromoleculeName: Casein kinase I isoform alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.842699 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ASSSGSKAEF IVGGKYKLVR KIGSGSFGDI YLAINITNGE EVAVKLESQK ARHPQLLYES KLYKILQGGV GIPHIRWYGQ EKDYNVLVM DLLGPSLEDL FNFCSRRFTM KTVLMLADQM ISRIEYVHTK NFIHRDIKPD NFLMGIGRHC NKLFLIDFGL A KKYRDNRT ...String:
ASSSGSKAEF IVGGKYKLVR KIGSGSFGDI YLAINITNGE EVAVKLESQK ARHPQLLYES KLYKILQGGV GIPHIRWYGQ EKDYNVLVM DLLGPSLEDL FNFCSRRFTM KTVLMLADQM ISRIEYVHTK NFIHRDIKPD NFLMGIGRHC NKLFLIDFGL A KKYRDNRT RQHIPYREDK NLTGTARYAS INAHLGIEQS RRDDMESLGY VLMYFNRTSL PWQGLKAATK KQKYEKISEK KM STPVEVL CKGFPAEFAM YLNYCRGLRF EEAPDYMYLR QLFRILFRTL NHQYDYTFDW TMLKQKAAQQ AASSSGQGQQ AQT PTGKQT DKTKSNMKGF

UniProtKB: Casein kinase I isoform alpha

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

MacromoleculeName: RNA (5'-R(P*UP*AP*AP*UP*AP*CP*UP*GP*CP*CP*UP*GP*GP*UP*AP*AP*UP*GP*AP*UP*GP*A)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.044219 KDa
SequenceString:
UAAUACUGCC UGGUAAUGAU GA

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Macromolecule #4: RNA (5'-R(P*AP*CP*CP*UP*AP*UP*CP*AP*GP*UP*AP*UP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*CP*CP*UP*AP*UP*CP*AP*GP*UP*AP*UP*UP*A)-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.392651 KDa
SequenceString:
ACCUAUCAGU AUUA

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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

BufferpH: 7.4 / Details: 25 mM HEPES pH 7.4, 100 mM NaCl, and 5 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU (ver. v 2.10.0.5)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8606 / Average electron dose: 76.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1338929
CTF correctionSoftware - Name: Warp (ver. v 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 314744
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.258)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.258)
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-10ji:
Structure of Human Argonaute2-miR200b RISC bound to 14nt long target in complex with kinase CK1alpha

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