3QX9

Crystal structure of MID domain from hAGO2 in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain.

Frank, F.Fabian, M.R.Stepinski, J.Jemielity, J.Darzynkiewicz, E.Sonenberg, N.Nagar, B.

(2011) Embo Rep. 12: 415-420

  • DOI: 10.1038/embor.2011.48
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In RNA silencing, microRNA (miRNA)-mediated translational repression occurs through mechanisms that do not invoke messenger-RNA (mRNA) target cleavage by Argonaute proteins. The nature of these mechanisms is unclear, but several recent studies have p ...

    In RNA silencing, microRNA (miRNA)-mediated translational repression occurs through mechanisms that do not invoke messenger-RNA (mRNA) target cleavage by Argonaute proteins. The nature of these mechanisms is unclear, but several recent studies have proposed that a direct interaction between the mRNA-cap and the middle (MID) domain of Argonautes is involved. Here, we present crystallographic and NMR data demonstrating that cap analogues do not bind significantly to the isolated MID domain of human Argonaute 2 (hAGO2) and are found in the miRNA 5'-nucleotide binding site in an implausible binding mode. Additionally, in vitro pull-down experiments with full-length hAGO2 indicate that the interaction with cap analogues is nonspecific.


    Organizational Affiliation

    Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute-2
A, B, C
138Homo sapiensMutation(s): 0 
Gene Names: AGO2 (EIF2C2)
EC: 3.1.26.n2
Find proteins for Q9UKV8 (Homo sapiens)
Go to Gene View: AGO2
Go to UniProtKB:  Q9UKV8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ATPKd: 90000 nM BINDINGMOAD
ATPKd: 90000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.494α = 87.14
b = 46.508β = 73.56
c = 65.817γ = 84.56
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-29
    Type: Database references