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- EMDB-75039: Human AGO2 bound to a miR-20a guide and a position 10-11 mismatch... -

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Basic information

Entry
Database: EMDB / ID: EMD-75039
TitleHuman AGO2 bound to a miR-20a guide and a position 10-11 mismatched target
Map dataStructure of human AGO2 in complex with 23 nt miR-20a guide and 18 nt, 10-11 mismatch target
Sample
  • Complex: Complex of human AGO2 bound to a guide miRNA (miR-20a) and a complementary target RNA with a position 10-11 mismatch to the guide.
    • RNA: Guide RNA
    • RNA: Target RNA
    • Protein or peptide: Protein argonaute-2
KeywordsComplex / RISC / RNAi / RNA BINDING PROTEIN
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: 3.02 Å
AuthorsSavidge A / Nakanishi K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Human AGO2 bound to a miR-20a guide and position 10-11 mismatched target
Authors: Zhang H / Annasaheb-Adhav V / Kehling C / Savidge A / Shen Z / Fu TM / Nakanishi K
History
DepositionJan 9, 2026-
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_75039.png

Downloads & links

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Map

FileDownload / File: emd_75039.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of human AGO2 in complex with 23 nt miR-20a guide and 18 nt, 10-11 mismatch target
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.36 Å/pix.
x 488 pix.
= 178.022 Å		0.36 Å/pix.
x 488 pix.
= 178.022 Å		0.36 Å/pix.
x 488 pix.
= 178.022 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.10920992 - 0.16635558
Average (Standard dev.)0.000127094 (±0.004698626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions488488488
Spacing488488488
CellA=B=C: 178.0224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75039_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of AGO2 complex

Fileemd_75039_half_map_1.map
AnnotationHalf map B of AGO2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of AGO2 complex

Fileemd_75039_half_map_2.map
AnnotationHalf map A of AGO2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human AGO2 bound to a guide miRNA (miR-20a) and a comp...

EntireName: Complex of human AGO2 bound to a guide miRNA (miR-20a) and a complementary target RNA with a position 10-11 mismatch to the guide.
Components
  • Complex: Complex of human AGO2 bound to a guide miRNA (miR-20a) and a complementary target RNA with a position 10-11 mismatch to the guide.
    • RNA: Guide RNA
    • RNA: Target RNA
    • Protein or peptide: Protein argonaute-2

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Supramolecule #1: Complex of human AGO2 bound to a guide miRNA (miR-20a) and a comp...

SupramoleculeName: Complex of human AGO2 bound to a guide miRNA (miR-20a) and a complementary target RNA with a position 10-11 mismatch to the guide.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guide RNA

MacromoleculeName: Guide RNA / type: rna / ID: 1 / Details: miRNA guide strand miR-20a-5p / 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: Target RNA

MacromoleculeName: Target RNA / type: rna / ID: 2
Details: Target RNA complementary to miR-20a-5p with a mismatch in positions 10-11
Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.684468 KDa
SequenceString:
CACUAACAGC 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: 98.881781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMDYKD DDDKMYSGAG PALAPPAPPP PIQGYAFKPP PRPDFGTSGR TIKLQANFFE MDIPKIDIYH YELDIKPEKC PRRVNREIV EHMVQHFKTQ IFGDRKPVFD GRKNLYTAMP LPIGRDKVEL EVTLPGEGKD RIFKVSIKWV SCVSLQALHD A LSGRLPSV ...String:
GAMGSMDYKD DDDKMYSGAG PALAPPAPPP PIQGYAFKPP PRPDFGTSGR TIKLQANFFE MDIPKIDIYH YELDIKPEKC PRRVNREIV EHMVQHFKTQ IFGDRKPVFD GRKNLYTAMP LPIGRDKVEL EVTLPGEGKD RIFKVSIKWV SCVSLQALHD A LSGRLPSV PFETIQALDV VMRHLPSMRY TPVGRSFFTA SEGCSNPLGG GREVWFGFHQ SVRPSLWKMM LNIDVSATAF YK AQPVIEF VCEVLDFKSI EEQQKPLTDS QRVKFTKEIK GLKVEITHCG QMKRKYRVCN VTRRPASHQT FPLQQESGQT VEC TVAQYF KDRHKLVLRY PHLPCLQVGQ EQKHTYLPLE VCNIVAGQRC IKKLTDNQTS TMIRATARSA PDRQEEISKL MRSA SFNTD PYVREFGIMV KDEMTDVTGR VLQPPSILYG GRNKAIATPV QGVWDMRNKQ FHTGIEIKVW AIACFAPQRQ CTEVH LKSF TEQLRKISRD AGMPIQGQPC FCKYAQGADS VEPMFRHLKN TYAGLQLVVV ILPGKTPVYA EVKRVGDTVL GMATQC VQM KNVQRTTPQT LSNLCLKINV KLGGVNNILL PQGRPPVFQQ PVIFLGADVT HPPAGDGKKP SIAAVVGSMD AHPNRYC AT VRVQQHRQEI IQDLAAMVRE LLIQFYKSTR FKPTRIIFYR DGVSEGQFQQ VLHHELLAIR EACIKLEKDY QPGITFIV V QKRHHTRLFC TDKNERVGKS GNIPAGTTVD TKITHPTEFD FYLCSHAGIQ GTSRPSHYHV LWDDNRFSSD ELQILTYQL CHTYVRCTRS VSIPAPAYYA HLVAFRARYH LVDKEHDSAE GSHTSGQSNG RDHQALAKAV QVHQDTLRTM YFA

UniProtKB: Protein argonaute-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6n4o

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 200460
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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