6MDZ | pdb_00006mdz

Human Argonaute2-miR-122 bound to a target RNA with two central mismatches (bu2)

• PDB DOI: https://doi.org/10.2210/pdb6MDZ/pdb
• NAKB: 6MDZ

• Classification: hydrolase/rna
• Organism(s): Homo sapiens, unidentified
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-09-05 Released: 2019-08-07 
• Deposition Author(s): Sheu-Gruttadauria, J., MacRae, I.J.
• 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: 3.40 Å
• R-Value Free: 
  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

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 75: 1243-1255.e7

• PubMed: 31353209 
• DOI: https://doi.org/10.1016/j.molcel.2019.06.019
• Primary Citation Related Structures: 
  6MDZ, 6MFN, 6MFR, 6NIT


• 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 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.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA. Electronic address: [e-mail].
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 223.11 kDa 
• Atom Count: 14,382 
• Modeled Residue Count: 1,674 
• Deposited Residue Count: 1,806 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A, B	859	Homo sapiens	Mutation(s): 6  Gene Names: AGO2, EIF2C2 EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV8 (Homo sapiens) Explore Q9UKV8  Go to UniProtKB:  Q9UKV8
PHAROS:  Q9UKV8 GTEx:  ENSG00000123908

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')	C, D	21	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')	E, F	23	unidentified

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	G [auth A], H [auth A], I [auth B], J [auth B]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.615	α = 90
b = 138.289	β = 90
c = 152.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Sheu-Gruttadauria, J., MacRae, I.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM104475
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115649

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description