6MFN

Human Argonaute2-miR-27a bound to HSUR1 target RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for Target-Directed MicroRNA Degradation.

Sheu-Gruttadauria, J.Pawlica, P.Klum, S.M.Wang, S.Yario, T.A.Schirle Oakdale, N.T.Steitz, J.A.MacRae, I.J.

(2019) Mol.Cell --: --

  • DOI: 10.1016/j.molcel.2019.06.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MicroRNAs (miRNAs) broadly regulate gene expression through association with Argonaute (Ago), which also protects miRNAs from degradation. However, miRNA stability is known to vary and is regulated by poorly understood mechanisms. A major emerging pr ...

    MicroRNAs (miRNAs) broadly regulate gene expression through association with Argonaute (Ago), which also protects miRNAs from degradation. However, miRNA stability is known to vary and is regulated by poorly understood mechanisms. A major emerging process, termed target-directed miRNA degradation (TDMD), employs specialized target RNAs to selectively bind to miRNAs and induce their decay. Here, we report structures of human Ago2 (hAgo2) bound to miRNAs and TDMD-inducing targets. miRNA and target form a bipartite duplex with an unpaired flexible linker. hAgo2 cannot physically accommodate the RNA, causing the duplex to bend at the linker and display the miRNA 3' end for enzymatic attack. Altering 3' end display by changing linker flexibility, changing 3' end complementarity, or mutationally inducing 3' end release impacts TDMD efficiency, leading to production of distinct 3'-miRNA isoforms in cells. Our results uncover the mechanism driving TDMD and reveal 3' end display as a key determinant regulating miRNA activity via 3' remodeling and/or degradation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA. Electronic address: joan.steitz@yale.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: macrae@scripps.edu.,Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute-2
A
859Homo sapiensMutation(s): 6 
Gene Names: AGO2 (EIF2C2)
EC: 3.1.26.n2
Find proteins for Q9UKV8 (Homo sapiens)
Go to Gene View: AGO2
Go to UniProtKB:  Q9UKV8
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*CP*AP*CP*AP*GP*UP*G)-3')C21Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*CP*UP*GP*UP*GP*AP*UP*AP*A)-3')E22synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPH
Query on IPH

Download SDF File 
Download CCD File 
A
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.948α = 90.00
b = 104.212β = 90.00
c = 152.858γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM104475
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM115649

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release