5FVG

Structure of IrisFP at 100 K.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein Irisfp.

Colletier, J.Sliwa, M.Gallat, F.Sugahara, M.Guillon, V.Schiro, G.Coquelle, N.Woodhouse, J.Roux, L.Gotthard, G.Royant, A.Uriarte, L.M.Ruckebusch, C.Joti, Y.Byrdin, M.Mizohata, E.Nango, E.Tanaka, T.Tono, K.Yabashi, M.Adam, V.Cammarata, M.Schlichting, I.Bourgeois, D.Weik, M.

(2016) J.Phys.Chem.Lett 7: 882

  • DOI: 10.1021/acs.jpclett.5b02789
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy ...

    Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.


    Organizational Affiliation

    Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.,RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1 , Rennes, France.,Max-Planck-Institut für medizinische Forschung , Jahnstrasse 29, 69120 Heidelberg, Germany.,The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France.,Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GREEN TO RED PHOTOCONVERTIBLE GFP-LIKE PROTEIN EOSFP
A, B, C, D
225Lobophyllia hemprichiiMutation(s): 0 
Find proteins for Q5S6Z9 (Lobophyllia hemprichii)
Go to UniProtKB:  Q5S6Z9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR8
Query on CR8
A, B, C, D
L-PEPTIDE LINKINGC17 H16 N5 O4HIS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.090α = 90.00
b = 96.320β = 90.00
c = 140.190γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection
  • Version 1.2: 2019-01-30
    Type: Data collection, Derived calculations, Experimental preparation
  • Version 1.3: 2019-02-06
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-10-23
    Type: Data collection, Database references, Derived calculations, Other