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

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1038/nchem.2853
  • Primary Citation of Related Structures:  
    5O89, 5O8A, 5O8B, 5O8C

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein246Aequorea victoriaMutation(s): 6 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42212
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PIA
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.53α = 90
b = 62.85β = 90
c = 71.76γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-01-17
    Changes: Refinement description