8VAJ

Human Argonaute3 bound to cityRNA and target RNA

• PDB DOI: https://doi.org/10.2210/pdb8VAJ/pdb
• NAKB: 8VAJ

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-12-11 Released: 2024-10-16 
• Deposition Author(s): Zhang, H., Sim, G., Adhav, V.A., Nakanishi, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.254 
• R-Value Work: 0.206 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Target cleavage and gene silencing by Argonautes with cityRNAs.

Zhang, H., Sim, G., Kehling, A.C., Adhav, V.A., Savidge, A., Pastore, B., Tang, W., Nakanishi, K.

(2024) Cell Rep 43: 114806-114806

• PubMed: 39368090 
• DOI: https://doi.org/10.1016/j.celrep.2024.114806
• Primary Citation of Related Structures:  
  8VAJ


• PubMed Abstract: 
  

  TinyRNAs (tyRNAs) are ≤17-nt guide RNAs associated with Argonaute proteins (AGOs), and certain 14-nt cleavage-inducing tyRNAs (cityRNAs) catalytically activate human Argonaute3 (AGO3). We present the crystal structure of AGO3 in complex with a cityRNA, 14-nt miR-20a, and its complementary target, revealing a different trajectory for the guide-target duplex from that of its ∼22-nt microRNA-associated AGO counterpart. cityRNA-loaded Argonaute2 (AGO2) and AGO3 enhance their endonuclease activity when the immediate 5' upstream region of the tyRNA target site (UTy) includes sequences with low affinity for AGO. We propose a model where cityRNA-loaded AGO2 and AGO3 efficiently cleave fully complementary tyRNA target sites unless they directly recognize the UTy. To investigate their gene silencing, we devised systems for loading endogenous AGOs with specific tyRNAs and demonstrated that, unlike microRNAs, cityRNA-mediated silencing heavily relies on target cleavage. Our study uncovered that AGO exploits cityRNAs for target recognition differently from microRNAs and alters gene silencing.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.2 kDa 
• Atom Count: 7,127 
• Modelled Residue Count: 849 
• Deposited Residue Count: 892 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-3	A	862	Homo sapiens	Mutation(s): 0  Gene Names: AGO3, EIF2C3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9G7 (Homo sapiens) Explore Q9H9G7  Go to UniProtKB:  Q9H9G7
PHAROS:  Q9H9G7 GTEx:  ENSG00000126070

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*G)-3')	B [auth E]	14	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*(SRA)P*AP*GP*CP*AP*CP*UP*UP*UP*AP*AP*A)-3')	C [auth F]	16	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.254 
• R-Value Work: 0.206 
• R-Value Observed: 0.211 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.142	α = 90
b = 138.126	β = 90
c = 143.533	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Zhang, H., Sim, G., Adhav, V.A., Nakanishi, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM138997

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release