9Q3G | pdb_00009q3g

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9Q3G

This is version 1.1 of the entry. See complete history

Literature

Neurodevelopmental disorder-linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3'→5' trimming.

Savidge, A.Zhang, H.Annasaheb Adhav, V.Kehling, A.C.Sim, G.Shen, Z.Fu, T.M.Nakanishi, K.

(2025) Proc Natl Acad Sci U S A 122: e2524644122-e2524644122

  • DOI: https://doi.org/10.1073/pnas.2524644122
  • Primary Citation Related Structures: 
    9Q3F, 9Q3G

  • PubMed 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 (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.


  • Organizational Affiliation
    • Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210.

Macromolecule Content 

  • Total Structure Weight: 100.4 kDa 
  • Atom Count: 6,480 
  • Modeled Residue Count: 793 
  • Deposited Residue Count: 879 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein argonaute-1871Homo sapiensMutation(s): 0 
Gene Names: AGO1EIF2C1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL18 (Homo sapiens)
Explore Q9UL18 
Go to UniProtKB:  Q9UL18
PHAROS:  Q9UL18
GTEx:  ENSG00000092847 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UL18
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
Non-homogenous guide RNA8Trichoplusia ni
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.7.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Data collection, Database references