ISDA: 8VAJ

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(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

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

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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.

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

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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