8VAJ image
Deposition Date 2023-12-11
Release Date 2024-10-16
Last Version Date 2024-10-16
Entry Detail
PDB ID:
8VAJ
Keywords:
RNA BINDING PROTEIN/RNA
Title:
Human Argonaute3 bound to cityRNA and target RNA
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Trichoplusia ni
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.45 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 2 21 21
8VAJ validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein argonaute-3
Gene (Uniprot):AGO3
Chain IDs:A
Chain Length:862
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H9G7 Pfam ID:PF16486, PF08699, PF02170, PF16488, PF16487, PF02171
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*G)-3')
Chain IDs:B (auth: E)
Chain Length:14
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*(SRA)P*AP*GP*CP*AP*CP*UP*UP*UP*AP*AP*A)-3')
Chain IDs:C (auth: F)
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Target cleavage and gene silencing by Argonautes with cityRNAs.
Cell Rep 43 114806 114806 (2024)
PMID: 39368090 DOI: 10.1016/j.celrep.2024.114806

Abstact

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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Primary Citation of related structures
8VAJ