4Z4F

Human Argonaute2 Bound to t1-DAP Target RNA

• PDB DOI: https://doi.org/10.2210/pdb4Z4F/pdb
• NAKB: 4Z4F

• Classification: gene regulation/rna
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2015-04-02 Released: 2015-09-23 
• Deposition Author(s): Schirle, N.T., MacRae, I.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.

Schirle, N.T., Sheu-Gruttadauria, J., Chandradoss, S.D., Joo, C., MacRae, I.J.

(2015) Elife 4

• PubMed: 26359634 
• DOI: https://doi.org/10.7554/eLife.07646
• Primary Citation of Related Structures:  
  4Z4C, 4Z4D, 4Z4E, 4Z4F, 4Z4G, 4Z4H, 4Z4I


• PubMed Abstract: 
  

  MicroRNAs (miRNAs) direct post-transcriptional regulation of human genes by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. An enigmatic feature of many conserved mammalian miRNA target sites is that an adenosine (A) nucleotide opposite miRNA nucleotide-1 confers enhanced target repression independently of base pairing potential to the miRNA. In this study, we show that human Argonaute2 (Ago2) possesses a solvated surface pocket that specifically binds adenine nucleobases in the 1 position (t1) of target RNAs. t1A nucleotides are recognized indirectly through a hydrogen-bonding network of water molecules that preferentially interacts with the N6 amine on adenine. t1A nucleotides are not utilized during the initial binding of Ago2 to its target, but instead function by increasing the dwell time on target RNA. We also show that N6 adenosine methylation blocks t1A recognition, revealing a possible mechanism for modulation of miRNA target site potency.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.

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: 107.83 kDa 
• Atom Count: 7,032 
• Modelled Residue Count: 829 
• Deposited Residue Count: 891 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A	859	Homo sapiens	Mutation(s): 1  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*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*UP*U)-3')	B	21	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*(N6G)P*A)-3')	C [auth D]	11	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	E [auth A], F [auth A], G [auth A]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
MG	D [auth A], H [auth B], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.859	α = 90
b = 116.591	β = 92.52
c = 70.375	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Schirle, N.T., MacRae, I.J.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description