6T39

Crystal structure of rsEGFP2 in its off-state determined by SFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 

wwPDB Validation   3D Report Full Report



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:  
    6T3A, 6T39

  • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinA250Aequorea victoriaMutation(s): 1 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PIA
Query on PIA
AL-PEPTIDE LINKINGC14 H15 N3 O4ALA, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.68α = 90
b = 62.89β = 90
c = 71.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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