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- PDB-9q3f: Structure of neurodevelopmental mutant AGO1 F180del in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9q3f
TitleStructure of neurodevelopmental mutant AGO1 F180del in complex with guide RNA
Components
  • Non-homogenous guide RNA
  • Protein argonaute-1
KeywordsGENE REGULATION / Complex / mutant
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 / Regulation of CDH1 mRNA translation by microRNAs / Transcriptional Regulation by MECP2 / RISC-loading complex / miRNA metabolic process ...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 / Regulation of CDH1 mRNA translation by microRNAs / Transcriptional Regulation by MECP2 / RISC-loading complex / miRNA metabolic process / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / 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 / Transcriptional Regulation by VENTX / nuclear-transcribed mRNA catabolic process / 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 / regulation of mRNA stability / negative regulation of angiogenesis / TP53 Regulates Metabolic Genes / P-body / Transcriptional regulation by small RNAs / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of non-canonical NF-kappaB signal transduction / Oncogene Induced Senescence / MAPK6/MAPK4 signaling / 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
RNA / Protein argonaute-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Trichoplusia ni (cabbage looper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSavidge, A. / Adhav, V. / Shen, Z. / Fu, T. / Nakanishi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Neurodevelopmental disorder-linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3'→5' trimming.
Authors: Andrew Savidge / Huaqun Zhang / Vishal Annasaheb Adhav / Audrey C Kehling / GeunYoung Sim / Zhangfei Shen / Tian-Min Fu / Kotaro Nakanishi /
Abstract: Mutations in Argonaute proteins (AGOs) cause Argonaute syndrome, a neurodevelopmental disorder (NDD), yet the underlying molecular mechanism remains unclear. We determined cryo-electron microscopy ...Mutations in Argonaute proteins (AGOs) cause Argonaute syndrome, a neurodevelopmental disorder (NDD), yet the underlying molecular mechanism remains unclear. We determined cryo-electron microscopy (cryo-EM) structures of wild-type (WT) AGO1 and the recurrent, severe causative ΔF180 mutant. AGO1(ΔF180) unexpectedly rearranges the hydrophobic core of the L1 domain to preserve the overall RNA-induced silencing complexes (RISC) architecture and recognize guide RNAs similarly to WT. Functionally, the mutant binds target RNAs like WT but more frequently retains passenger strands, implicating a defect in RISC assembly. Biochemical assays of ΔF180 and L190P mutants revealed normal duplex loading but impaired passenger ejection, exposing guide 3' ends to 3'→5' exonucleases and generating abnormally short ~11-nucleotide RNAs. In cells, AGO1(ΔF180), AGO1(G199S), and corresponding AGO2 mutants likewise produced truncated guides. Together, these findings support a model in which defective passenger ejection underlies the pathology of AGO-associated NDDs by rendering microRNAs bound to AGO syndrome mutants susceptible to aberrant 3' trimming.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
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Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1May 6, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1May 6, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein argonaute-1
B: Non-homogenous guide RNA


Theoretical massNumber of molelcules
Total (without water)101,3222
Polymers101,3222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein argonaute-1 / Argonaute1 / hAgo1 / Argonaute RISC catalytic component 1 / Eukaryotic translation initiation ...Argonaute1 / hAgo1 / Argonaute RISC catalytic component 1 / Eukaryotic translation initiation factor 2C 1 / eIF-2C 1 / eIF2C 1 / Putative RNA-binding protein Q99


Mass: 98733.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal FLAG-tag, deletion of F180 / Source: (gene. exp.) Homo sapiens (human) / Gene: AGO1, EIF2C1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UL18
#2: RNA chain Non-homogenous guide RNA


Mass: 2588.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Production host: Trichoplusia ni (cabbage looper)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of human Argonaute1 F180Deletion bound to a non-homogenous guide RNA
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.106 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES pH 7.5C8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.5 mMTCEPC9H15O6P1
42 mMBS3C16H18N2Na2O14S21
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -500 nm
Image recordingAverage exposure time: 2.75 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2PHENIX1.20.1_4487model refinement
3EPUimage acquisition
5cryoSPARC4.7.0CTF correction
10cryoSPARC4.7.0initial Euler assignment
11cryoSPARC4.7.0final Euler assignment
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435426 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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