3QX8

Crystal structure of MID domain from hAGO2 in complex with m7GpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/embor.2011.48
  • Primary Citation of Related Structures:  
    3QX8, 3QX9

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein argonaute-2
A, B, C
138Homo sapiensMutation(s): 0 
Gene Names: EIF2C2AGO2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV8 (Homo sapiens)
Explore Q9UKV8 
Go to UniProtKB:  Q9UKV8
PHAROS:  Q9UKV8
GTEx:  ENSG00000123908 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKV8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
GTG PDBBind:  3QX8 Kd: 1.37e+6 (nM) from 1 assay(s)
Binding MOAD:  3QX8 Kd: 1.37e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • R-Value Observed: 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
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-29
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description