Structure of mEos4b in the green long-lived dark state

Experimental Data Snapshot

  • Resolution: 2.41 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

This is version 3.0 of the entry. See complete history


Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State.

De Zitter, E.Ridard, J.Thedie, D.Adam, V.Levy, B.Byrdin, M.Gotthard, G.Van Meervelt, L.Dedecker, P.Demachy, I.Bourgeois, D.

(2020) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.0c01880
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Green-to-red photoconvertible fluorescent proteins (PCFPs) are key players in advanced microscopy schemes such as photoactivated localization microscopy (PALM). Whereas photoconversion and red-state blinking in PCFPs have been studied intensively, their green-state photophysical behavior has received less attention. Yet dark states in green PCFPs can become strongly populated in PALM schemes and exert an indirect but considerable influence on the quality of data recorded in the red channel. Furthermore, green-state photoswitching in PCFPs can be used directly for PALM and has been engineered to design highly efficient reversibly switchable fluorescent proteins (RSFPs) amenable to various nanoscopy schemes. Here, we demonstrate that green mEos4b efficiently switches to a long-lived dark state through cis - trans isomerization of its chromophore, as do most RSFPs. However, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy, we find that the dark state in green mEos4b is much more dynamic than that seen in switched-off green IrisFP, a biphotochromic PCFP engineered from the common EosFP parent. Our data suggest that H-bonding patterns maintained by the chromophore in green PCFPs and RSFPs in both their on- and off-states collectively control photoswitching quantum yields. The reduced number of H-bonds maintained by the dynamic dark chromophore in green mEos4b thus largely accounts for the observed lower switching contrast as compared to that of IrisFP. We also compare the long-lived dark states reached from green and red mEos4b, on the basis of their X-ray structures and Raman signatures. Altogether, these data provide a unifying picture of the complex photophysics of PCFPs and RSFPs.

  • Organizational Affiliation

    Department of Chemistry, KU Leuven, Heverlee 3001, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green to red photoconvertible GFP-like protein EosFP257Lobophyllia hemprichiiMutation(s): 14 
Find proteins for Q5S6Z9 (Lobophyllia hemprichii)
Explore Q5S6Z9 
Go to UniProtKB:  Q5S6Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5S6Z9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.41 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.62α = 90
b = 57.66β = 90
c = 102.4γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgium--
Grenoble Instruct-ERIC CenterFranceUMS 3518 CNRS-CEA-UGA-EMBL

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 2.0: 2021-09-01
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations