5WEA

Human Argonaute2 Helix-7 Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition.

Klum, S.M.Chandradoss, S.D.Schirle, N.T.Joo, C.MacRae, I.J.

(2018) EMBO J. 37: 75-88

  • DOI: 10.15252/embj.201796474

  • PubMed Abstract: 
  • Argonaute proteins use microRNAs (miRNAs) to identify mRNAs targeted for post-transcriptional repression. Biochemical assays have demonstrated that Argonaute functions by modulating the binding properties of its miRNA guide so that pairing to the see ...

    Argonaute proteins use microRNAs (miRNAs) to identify mRNAs targeted for post-transcriptional repression. Biochemical assays have demonstrated that Argonaute functions by modulating the binding properties of its miRNA guide so that pairing to the seed region is exquisitely fast and accurate. However, the mechanisms used by Argonaute to reshape the binding properties of its small RNA guide remain poorly understood. Here, we identify a structural element, α-helix-7, in human Argonaute2 (Ago2) that is required for speed and fidelity in binding target RNAs. Biochemical, structural, and single-molecule data indicate that helix-7 acts as a molecular wedge that pivots to enforce rapid making and breaking of miRNA:target base pairs in the 3' half of the seed region. These activities allow Ago2 to rapidly dismiss off-targets and dynamically search for seed-matched sites at a rate approaching the limit of diffusion.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein argonaute-2
A
859Homo sapiensGene Names: AGO2 (EIF2C2)
EC: 3.1.26.n2
Find proteins for Q9UKV8 (Homo sapiens)
Go to Gene View: AGO2
Go to UniProtKB:  Q9UKV8
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*U)-3')B8synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPH
Query on IPH

Download SDF File 
Download CCD File 
A
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.261α = 90.00
b = 107.880β = 107.46
c = 68.723γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM104475
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM115649

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence
  • Version 1.2: 2018-01-17
    Type: Database references