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- EMDB-75217: Structure of Human Argonaute2-miR200b RISC bound to 14nt long tar... -

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Basic information

Entry
Database: EMDB / ID: EMD-75217
TitleStructure of Human Argonaute2-miR200b RISC bound to 14nt long target RNA
Map data
Sample
  • Complex: Human Argonaute2-miR200 complex bound with 14nt target RNA
    • Protein or peptide: Protein argonaute-2
    • 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 / RNA binding protein / RNA / HYDROLASE-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 / miRNA processing / mRNA cap binding / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / miRNA-mediated gene silencing by inhibition of translation / regulatory ncRNA-mediated gene silencing / pre-miRNA processing / RNA 7-methylguanosine cap binding / regulation of synapse maturation / 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 / 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 / RNA endonuclease activity / Nuclear events stimulated by ALK signaling in cancer / translation initiation factor activity / negative regulation of translational initiation / TP53 Regulates Metabolic Genes / positive regulation of translation / Transcriptional regulation by small RNAs / P-body / 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 / postsynapse / single-stranded RNA binding / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / 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: 3.4 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 RNA
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_75217.png

Downloads & links

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Map

FileDownload / File: emd_75217.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.07621215 - 0.2987184
Average (Standard dev.)0.0022071525 (±0.014280059)
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_75217_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer modified

Fileemd_75217_additional_2.map
AnnotationDeepEMhancer modified
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75217_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75217_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human Argonaute2-miR200 complex bound with 14nt target RNA

EntireName: Human Argonaute2-miR200 complex bound with 14nt target RNA
Components
  • Complex: Human Argonaute2-miR200 complex bound with 14nt target RNA
    • Protein or peptide: Protein argonaute-2
    • 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: Human Argonaute2-miR200 complex bound with 14nt target RNA

SupramoleculeName: Human Argonaute2-miR200 complex bound with 14nt target RNA
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: 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: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.044219 KDa
SequenceString:
UAAUACUGCC UGGUAAUGAU GA

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Macromolecule #3: 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: 3 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 418084
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-10jh:
Structure of Human Argonaute2-miR200b RISC bound to 14nt long target RNA

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