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- EMDB-72193: Cryo-EM structure of human AGO1 in complex with guide RNA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72193
TitleCryo-EM structure of human AGO1 in complex with guide RNA
Map dataMap of WT human Argonaute1
Sample
  • Complex: Complex of human Argonaute1 bound to a non-homogenous guide RNA
    • Protein or peptide: Protein argonaute-1
    • RNA: Non-homogenous guide RNA
KeywordsComplex / GENE REGULATION
Function / homology
Function and homology information


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 / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RISC-loading complex / miRNA metabolic process / RISC complex assembly ...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 / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RISC-loading complex / miRNA metabolic process / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / RNA polymerase II complex binding / nuclear-transcribed mRNA catabolic process / Transcriptional Regulation by VENTX / Regulation of MECP2 expression and activity / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of mRNA stability / negative regulation of angiogenesis / TP53 Regulates Metabolic Genes / P-body / Transcriptional regulation by small RNAs / positive regulation of non-canonical NF-kappaB signal transduction / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSavidge A / Adhav V / Shen Z / Fu T / 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: Cryo-EM structure of human AGO1 in complex with guide RNA
Authors: Savidge A / Zhang H / Adhav V / Kehling A / Shen Z / Fu T / Nakanishi K
History
DepositionAug 18, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72193.png

Downloads & links

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Map

FileDownload / File: emd_72193.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of WT human Argonaute1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.45 Å/pix.
x 488 pix.
= 218.624 Å		0.45 Å/pix.
x 488 pix.
= 218.624 Å		0.45 Å/pix.
x 488 pix.
= 218.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.448 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.14142393 - 0.21786667
Average (Standard dev.)0.000022403372 (±0.0051284013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions488488488
Spacing488488488
CellA=B=C: 218.62401 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72193_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 WT human Argonaute1

Fileemd_72193_half_map_1.map
AnnotationHalf map B WT human Argonaute1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A WT human Argonaute1

Fileemd_72193_half_map_2.map
AnnotationHalf map A WT human Argonaute1
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 Argonaute1 bound to a non-homogenous guide RNA

EntireName: Complex of human Argonaute1 bound to a non-homogenous guide RNA
Components
  • Complex: Complex of human Argonaute1 bound to a non-homogenous guide RNA
    • Protein or peptide: Protein argonaute-1
    • RNA: Non-homogenous guide RNA

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Supramolecule #1: Complex of human Argonaute1 bound to a non-homogenous guide RNA

SupramoleculeName: Complex of human Argonaute1 bound to a non-homogenous guide RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106 KDa

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Macromolecule #1: Protein argonaute-1

MacromoleculeName: Protein argonaute-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.880906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMDYKD DDDKMEAGPS GAAAGAYLPP LQQVFQAPRR PGIGTVGKPI KLLANYFEVD IPKIDVYHYE VDIKPDKCPR RVNREVVEY MVQHFKPQIF GDRKPVYDGK KNIYTVTALP IGNERVDFEV TIPGEGKDRI FKVSIKWLAI VSWRMLHEAL V SGQIPVPL ...String:
GAMGSMDYKD DDDKMEAGPS GAAAGAYLPP LQQVFQAPRR PGIGTVGKPI KLLANYFEVD IPKIDVYHYE VDIKPDKCPR RVNREVVEY MVQHFKPQIF GDRKPVYDGK KNIYTVTALP IGNERVDFEV TIPGEGKDRI FKVSIKWLAI VSWRMLHEAL V SGQIPVPL ESVQALDVAM RHLASMRYTP VGRSFFSPPE GYYHPLGGGR EVWFGFHQSV RPAMWKMMLN IDVSATAFYK AQ PVIEFMC EVLDIRNIDE QPKPLTDSQR VRFTKEIKGL KVEVTHCGQM KRKYRVCNVT RRPASHQTFP LQLESGQTVE CTV AQYFKQ KYNLQLKYPH LPCLQVGQEQ KHTYLPLEVC NIVAGQRCIK KLTDNQTSTM IKATARSAPD RQEEISRLMK NASY NLDPY IQEFGIKVKD DMTEVTGRVL PAPILQYGGR NRAIATPNQG VWDMRGKQFY NGIEIKVWAI ACFAPQKQCR EEVLK NFTD QLRKISKDAG MPIQGQPCFC KYAQGADSVE PMFRHLKNTY SGLQLIIVIL PGKTPVYAEV KRVGDTLLGM ATQCVQ VKN VVKTSPQTLS NLCLKINVKL GGINNILVPH QRSAVFQQPV IFLGADVTHP PAGDGKKPSI TAVVGSMDAH PSRYCAT VR VQRPRQEIIE DLSYMVRELL IQFYKSTRFK PTRIIFYRDG VPEGQLPQIL HYELLAIRDA CIKLEKDYQP GITYIVVQ K RHHTRLFCAD KNERIGKSGN IPAGTTVDTN ITHPFEFDFY LCSHAGIQGT SRPSHYYVLW DDNRFTADEL QILTYQLCH TYVRCTRSVS IPAPAYYARL VAFRARYHLV DKEHDSGEGS HISGQSNGRD PQALAKAVQV HQDTLRTMYF A

UniProtKB: Protein argonaute-1

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Macromolecule #2: Non-homogenous guide RNA

MacromoleculeName: Non-homogenous guide RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 1.523801 KDa
SequenceString:
(N)(N)(N)(N)(N)(N)(N)(N)

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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

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES pH 7.5
150.0 mMNaClsodium chloride
0.5 mMC9H15O6PTCEP
2.0 mMC16H18N2Na2O14S2BS3
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.75 sec. / 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: -2.5 µm / Nominal defocus min: -0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4kxt


Details: The crystal structure of 4KXT was used as the starting model for the cryo-EM structure.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 276867
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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