3LUH

Crystal structure of MID domain from hAGO2 in complex with GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2.

Frank, F.Sonenberg, N.Nagar, B.

(2010) Nature 465: 818-822

  • DOI: 10.1038/nature09039
  • Primary Citation of Related Structures:  3LUC, 3LUD, 3LUG, 3LUJ, 3LUK

  • PubMed Abstract: 
  • MicroRNAs (miRNAs) mediate post-transcriptional gene regulation through association with Argonaute proteins (AGOs). Crystal structures of archaeal and bacterial homologues of AGOs have shown that the MID (middle) domain mediates the interaction with ...

    MicroRNAs (miRNAs) mediate post-transcriptional gene regulation through association with Argonaute proteins (AGOs). Crystal structures of archaeal and bacterial homologues of AGOs have shown that the MID (middle) domain mediates the interaction with the phosphorylated 5' end of the miRNA guide strand and this interaction is thought to be independent of the identity of the 5' nucleotide in these systems. However, analysis of the known sequences of eukaryotic miRNAs and co-immunoprecipitation experiments indicate that there is a clear bias for U or A at the 5' position. Here we report the crystal structure of a MID domain from a eukaryotic AGO protein, human AGO2. The structure, in complex with nucleoside monophosphates (AMP, CMP, GMP, and UMP) mimicking the 5' end of miRNAs, shows that there are specific contacts made between the base of UMP or AMP and a rigid loop in the MID domain. Notably, the structure of the loop discriminates against CMP and GMP and dissociation constants calculated from NMR titration experiments confirm these results, showing that AMP (0.26 mM) and UMP (0.12 mM) bind with up to 30-fold higher affinity than either CMP (3.6 mM) or GMP (3.3 mM). This study provides structural evidence for nucleotide-specific interactions in the MID domain of eukaryotic AGO proteins and explains the observed preference for U or A at the 5' end of miRNAs.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute-2
A, B, C
138Homo sapiensGene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
5GP
Query on 5GP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5GPKd: 3300000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.433α = 86.06
b = 46.971β = 72.77
c = 66.352γ = 83.70
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
CNSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance