5FVI

Structure of IrisFP in mineral grease at 100 K.

• PDB DOI: https://doi.org/10.2210/pdb5FVI/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Lobophyllia hemprichii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-02-07 Released: 2016-04-13 
• Deposition Author(s): Colletier, J.P., Gallat, F.X., Coquelle, N., Weik, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

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 7: 882

• PubMed: 26866390 
• DOI: https://doi.org/10.1021/acs.jpclett.5b02789
• Primary Citation of Related Structures:  
  5FVF, 5FVG, 5FVI


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.63 kDa 
• Atom Count: 8,618 
• Modelled Residue Count: 889 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green to red photoconvertible GFP-like protein EosFP	A, B, C, D	223	Lobophyllia hemprichii	Mutation(s): 3
UniProt
Find proteins for Q5S6Z9 (Lobophyllia hemprichii) Explore Q5S6Z9  Go to UniProtKB:  Q5S6Z9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5SQ	A, B, C, D	L-PEPTIDE LINKING	C17 H17 N5 O4		HIS, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.58	α = 90
b = 95.94	β = 90
c = 139.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Colletier, J.P., Gallat, F.X., Coquelle, N., Weik, M.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Advisory, Data collection
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-10-23
  Changes: Data collection, Database references, Derived calculations, Other
• Version 2.0: 2021-09-01
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.1: 2024-01-10
  Changes: Refinement description