6T3A

Difference-refined structure of rsEGFP2 10 ns following 400-nm laser irradiation of the off-state determined by SFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy.

Woodhouse, J.Nass Kovacs, G.Coquelle, N.Uriarte, L.M.Adam, V.Barends, T.R.M.Byrdin, M.de la Mora, E.Bruce Doak, R.Feliks, M.Field, M.Fieschi, F.Guillon, V.Jakobs, S.Joti, Y.Macheboeuf, P.Motomura, K.Nass, K.Owada, S.Roome, C.M.Ruckebusch, C.Schiro, G.Shoeman, R.L.Thepaut, M.Togashi, T.Tono, K.Yabashi, M.Cammarata, M.Foucar, L.Bourgeois, D.Sliwa, M.Colletier, J.P.Schlichting, I.Weik, M.

(2020) Nat Commun 11: 741-741

  • DOI: 10.1038/s41467-020-14537-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Reversibly switchable fluorescent proteins (RSFPs) serve as markers in advanced fluorescence imaging. Photoswitching from a non-fluorescent off-state to a fluorescent on-state involves trans-to-cis chromophore isomerization and proton transfer. Where ...

    Reversibly switchable fluorescent proteins (RSFPs) serve as markers in advanced fluorescence imaging. Photoswitching from a non-fluorescent off-state to a fluorescent on-state involves trans-to-cis chromophore isomerization and proton transfer. Whereas excited-state events on the ps timescale have been structurally characterized, conformational changes on slower timescales remain elusive. Here we describe the off-to-on photoswitching mechanism in the RSFP rsEGFP2 by using a combination of time-resolved serial crystallography at an X-ray free-electron laser and ns-resolved pump-probe UV-visible spectroscopy. Ten ns after photoexcitation, the crystal structure features a chromophore that isomerized from trans to cis but the surrounding pocket features conformational differences compared to the final on-state. Spectroscopy identifies the chromophore in this ground-state photo-intermediate as being protonated. Deprotonation then occurs on the μs timescale and correlates with a conformational change of the conserved neighbouring histidine. Together with a previous excited-state study, our data allow establishing a detailed mechanism of off-to-on photoswitching in rsEGFP2.


    Organizational Affiliation

    Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000, Grenoble, France. weik@ibs.fr.,Laboratoire Chimie et Biologie des Métaux, BIG, CEA-Grenoble, Grenoble, France.,RIKEN SPring-8 Center, Sayo, Japan.,Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000, Lille, France. michel.sliwa@univ-lille.fr.,Large-Scale Structures Group, Institut Laue Langevin, 71, avenue des Martyrs, 38042, Grenoble, cedex 9, France.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan.,Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany.,Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Rennes, France.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany. ilme.schlichting@mpimf-heidelberg.mpg.de.,Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000, Grenoble, France.,Department of Chemistry, University of Southern California, Los Angeles, USA.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000, Lille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
252Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PIA
Query on PIA
A
L-PEPTIDE LINKINGC14 H15 N3 O4ALA,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.680α = 90.00
b = 62.890β = 90.00
c = 71.710γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PHASERphasing
PHENIXrefinement
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE32-0004

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release