7O7W

Crystal structure of rsEGFP2 mutant V151L in the non-fluorescent off-state the determined by serial femtosecond crystallography at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement.

Adam, V.Hadjidemetriou, K.Jensen, N.Shoeman, R.L.Woodhouse, J.Aquila, A.Banneville, A.S.Barends, T.R.M.Bezchastnov, V.Boutet, S.Byrdin, M.Cammarata, M.Carbajo, S.Eleni Christou, N.Coquelle, N.De la Mora, E.El Khatib, M.Moreno Chicano, T.Bruce Doak, R.Fieschi, F.Foucar, L.Glushonkov, O.Gorel, A.Grunbein, M.L.Hilpert, M.Hunter, M.Kloos, M.Koglin, J.E.Lane, T.J.Liang, M.Mantovanelli, A.Nass, K.Nass Kovacs, G.Owada, S.Roome, C.M.Schiro, G.Seaberg, M.Stricker, M.Thepaut, M.Tono, K.Ueda, K.Uriarte, L.M.You, D.Zala, N.Domratcheva, T.Jakobs, S.Sliwa, M.Schlichting, I.Colletier, J.P.Bourgeois, D.Weik, M.

(2022) Chemphyschem 23: e202200192-e202200192

  • DOI: https://doi.org/10.1002/cphc.202200192
  • Primary Citation of Related Structures:  
    7AMB, 7AMF, 7O7C, 7O7D, 7O7E, 7O7H, 7O7U, 7O7V, 7O7W, 7O7X

  • PubMed Abstract: 

    Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.


  • Organizational Affiliation

    Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein250Aequorea victoriaMutation(s): 7 
Gene Names: GFP
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PIA
Query on PIA
A
L-PEPTIDE LINKINGC14 H15 N3 O4ALA, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.85α = 90
b = 62.93β = 90
c = 72.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2022-10-19
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description