5AAO

Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools.

Schutz, M.Batyuk, A.Klenk, C.Kummer, L.de Picciotto, S.Gulbakan, B.Wu, Y.Newby, G.A.Zosel, F.Schoppe, J.Sedlak, E.Mittl, P.R.Zenobi, R.Wittrup, K.D.Pluckthun, A.

(2016) J. Mol. Biol. 428: 1272-1289

  • DOI: 10.1016/j.jmb.2016.01.017

  • PubMed Abstract: 
  • Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biolo ...

    Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biological molecules of interest. Recently, a novel class of fluorescence-based probes, fluorogen-activating proteins (FAPs), has been reported. These binding proteins are based on antibody single-chain variable fragments and activate fluorogenic dyes, which only become fluorescent upon activation and do not fluoresce when free in solution. Here we present a novel class of fluorogen activators, termed FADAs, based on the very robust designed ankyrin repeat protein scaffold, which also readily folds in the reducing environment of the cytoplasm. The FADA generated in this study was obtained by combined selections with ribosome display and yeast surface display. It enhances the fluorescence of malachite green (MG) dyes by a factor of more than 11,000 and thus activates MG to a similar extent as FAPs based on single-chain variable fragments. As shown by structure determination and in vitro measurements, this FADA was evolved to form a homodimer for the activation of MG dyes. Exploiting the favorable properties of the designed ankyrin repeat protein scaffold, we created a FADA biosensor suitable for imaging of proteins on the cell surface, as well as in the cytosol. Moreover, based on the requirement of dimerization for strong fluorogen activation, a prototype FADA biosensor for in situ detection of a target protein and protein-protein interactions was developed. Therefore, FADAs are versatile fluorescent probes that are easily produced and suitable for diverse applications and thus extend the FAP technology.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, CH-8057, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAD3210
A, B, C, D, E, F, G, H, I, J, K, L
169N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6FE
Query on 6FE

Download SDF File 
Download CCD File 
A, C, E, G, J, K
4-[[4-(dimethylamino)cyclohexa-2,5-dien-1-ylidene]-(4-methoxyphenyl)methyl]-N,N-dimethyl-aniline
MALACHITE GREEN DERIVATIVE MG-2P
C24 H28 N2 O
FEUHGUIYUWEJCH-JHGYQWQCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.512α = 90.00
b = 109.754β = 94.35
c = 100.301γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references