3QX8

Crystal structure of MID domain from hAGO2 in complex with m7GpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 

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
GTG
Query on GTG

Download SDF File 
Download CCD File 
A, B, C
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
MRNA CAP ANALOG N7-METHYL GPPPG
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GTGKd: 1370000 nM BINDINGMOAD
GTGKd: 1370000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.686α = 86.09
b = 46.967β = 73.33
c = 66.119γ = 83.38
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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