5EJU | pdb_00005eju

Ensemble refinement of the Crystal Structure of the Reversibly photoswitching chromoprotein Dathail, Ground State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.194 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5EJU

This is version 3.0 of the entry. See complete history

Literature

Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail.

Langan, P.S.Close, D.W.Coates, L.Rocha, R.C.Ghosh, K.Kiss, C.Waldo, G.Freyer, J.Kovalevsky, A.Bradbury, A.R.

(2016) J Mol Biology 428: 1776-1789

  • DOI: https://doi.org/10.1016/j.jmb.2016.02.029
  • Primary Citation Related Structures: 
    5EB6, 5EB7, 5EBJ, 5EJU, 5EXU

  • PubMed Abstract: 

    We report the engineering of a new reversibly switching chromogenic protein, Dathail. Dathail was evolved from the extremely thermostable fluorescent proteins thermal green protein (TGP) and eCGP123 using directed evolution and ratiometric sorting. Dathail has two spectrally distinct chromogenic states with low quantum yields, corresponding to absorbance in a ground state with a maximum at 389nm, and a photo-induced metastable state with a maximum at 497nm. In contrast to all previously described photoswitchable proteins, both spectral states of Dathail are non-fluorescent. The photo-induced chromogenic state of Dathail has a lifetime of ~50min at 293K and pH7.5 as measured by UV-Vis spectrophotometry, returning to the ground state through thermal relaxation. X-ray crystallography provided structural insights supporting a change in conformation and coordination in the chromophore pocket as being responsible for Dathail's photoswitching. Neutron crystallography, carried out for the first time on a protein from the green fluorescent protein family, showed a distribution of hydrogen atoms revealing protonation of the chromophore 4-hydroxybenzyl group in the ground state. The neutron structure also supports the hypothesis that the photo-induced proton transfer from the chromophore occurs through water-mediated proton relay into the bulk solvent. Beyond its spectroscopic curiosity, Dathail has several characteristics that are improvements for applications, including low background fluorescence, large spectral separation, rapid switching time, and the ability to switch many times. Therefore, Dathail is likely to be extremely useful in the quickly developing fields of imaging and biosensors, including photochromic Förster resonance energy transfer, high-resolution microscopy, and live tracking within the cell.


  • Organizational Affiliation
    • Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; Nanoscience and Microsystems Engineering, University of New Mexico, Albuquerque, NM 87131, USA.

Macromolecule Content 

  • Total Structure Weight: 25.9 kDa 
  • Atom Count: 1,910 
  • Modeled Residue Count: 214 
  • Deposited Residue Count: 229 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reversibly photoswitching protein Dathail229synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRQ
Query on CRQ
A
L-PEPTIDE LINKINGC16 H16 N4 O5GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.194 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.97α = 90
b = 81.09β = 90
c = 39.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Cootmodel building
HKL-3000data collection
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Structure summary
  • Version 3.0: 2026-03-18
    Changes: Polymer sequence