5O8B

Difference-refined excited-state structure of rsEGFP2 1ps following 400nm-laser irradiation of the off-state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.290 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography.

Coquelle, N.Sliwa, M.Woodhouse, J.Schiro, G.Adam, V.Aquila, A.Barends, T.R.M.Boutet, S.Byrdin, M.Carbajo, S.De la Mora, E.Doak, R.B.Feliks, M.Fieschi, F.Foucar, L.Guillon, V.Hilpert, M.Hunter, M.S.Jakobs, S.Koglin, J.E.Kovacsova, G.Lane, T.J.Levy, B.Liang, M.Nass, K.Ridard, J.Robinson, J.S.Roome, C.M.Ruckebusch, C.Seaberg, M.Thepaut, M.Cammarata, M.Demachy, I.Field, M.Shoeman, R.L.Bourgeois, D.Colletier, J.P.Schlichting, I.Weik, M.

(2018) Nat Chem 10: 31-37

  • DOI: 10.1038/nchem.2853
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptio ...

    Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.


    Organizational Affiliation

    Laboratoire de Chimie-Physique, CNRS/University Paris-Sud, University Paris-Saclay, UMR 8000, 91405 Orsay, France.,Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France.,Department of NanoBiophotonics, Max-Planck-Institut für biophysikalische Chemie, 37077 Göttingen, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.,Laboratoire de Spectrochimie Infrarouge et Raman, Université de Lille, CNRS, UMR 8516, LASIR, F59 000 Lille, France.,Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, California 94025, USA.,Department of Physics, University of Rennes 1, UMR UR1-CNRS 6251, Rennes, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
248Aequorea victoriaMutation(s): 5 
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: 1.7 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.290 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.530α = 90.00
b = 62.850β = 90.00
c = 71.760γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata scaling
PHASERphasing
PHENIXrefinement
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Data collection
  • Version 1.2: 2019-10-16
    Type: Data collection