3VNA

Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains

Zha, X.Xia, Q.Yuan, Y.A.

(2012) Febs Lett. 586: 3200-3207

  • DOI: 10.1016/j.febslet.2012.06.038
  • Primary Citation of Related Structures:  3VNB

  • PubMed Abstract: 
  • The RISC-associated Argonaute (Ago) proteins play the catalytic role for RISC-mediated gene regulation by selecting small RNAs and subsequent targeting and cleavage of complementary mRNAs. Ago Mid domains are proposed to play essential roles in small ...

    The RISC-associated Argonaute (Ago) proteins play the catalytic role for RISC-mediated gene regulation by selecting small RNAs and subsequent targeting and cleavage of complementary mRNAs. Ago Mid domains are proposed to play essential roles in small RNA sorting. Here, we report the crystal structures of Arabidopsis Ago1 Mid domain and its chimera mutant with part of Ago1 replaced by Ago4. The structures demonstrate that a single amino insertion in the nucleotide specificity loop of AtAgo1 will change the nucleotide binding preference of AtAgo1 from "5'-U" to "5'-A". Moreover, we identify a long positively charged groove located along the "5'-end-nucleotide specificity loop" and occupied by several sulfate ions with the distance of 9-11Å distance, indicating a putative mRNA target binding groove.


    Organizational Affiliation

    Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute 1
A
154Arabidopsis thalianaGene Names: AGO1
Find proteins for O04379 (Arabidopsis thaliana)
Go to Gene View: AGO1
Go to UniProtKB:  O04379
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.005α = 90.00
b = 60.966β = 90.00
c = 67.376γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-01-11 
  • Released Date: 2012-10-10 
  • Deposition Author(s): Yuan, Y.A., Zha, X.

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release