5O8A | pdb_00005o8a

Crystal Structure of rsEGFP2 in the non-fluorescent off-state determined by SFX

• PDB DOI: https://doi.org/10.2210/pdb5O8A/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-12 Released: 2017-09-27 
• Deposition Author(s): 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., 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.184 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 29256511 
• DOI: https://doi.org/10.1038/nchem.2853
• Primary Citation 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.

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Organizational Affiliation: 
• Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France.
Laboratoire de Spectrochimie Infrarouge et Raman, Université de Lille, CNRS, UMR 8516, LASIR, F59 000 Lille, France.
Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, California 94025, USA.
Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
Department of NanoBiophotonics, Max-Planck-Institut für biophysikalische Chemie, 37077 Göttingen, Germany.
Laboratoire de Chimie-Physique, CNRS/University Paris-Sud, University Paris-Saclay, UMR 8000, 91405 Orsay, France.
Department of Physics, University of Rennes 1, UMR UR1-CNRS 6251, Rennes, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.1 kDa 
• Atom Count: 4,233 
• Modeled Residue Count: 244 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	246	Aequorea victoria	Mutation(s): 6  Gene Names: GFP
UniProt
Find proteins for A0A1S5SHT2 (Human respiratory syncytial virus) Explore A0A1S5SHT2  Go to UniProtKB:  A0A1S5SHT2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PIA	A	L-PEPTIDE LINKING	C14 H15 N3 O4		ALA, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.184 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1369547

Diffraction Data: https://doi.org/10.11577/1369546

Diffraction Data: https://doi.org/10.11577/1369542

Diffraction Data: https://doi.org/10.11577/1369545

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.53	α = 90
b = 62.85	β = 90
c = 71.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): 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., 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.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.2: 2017-12-27
  Changes: Database references
• Version 1.3: 2018-11-14
  Changes: Data collection
• Version 1.4: 2019-10-16
  Changes: Data collection
• Version 1.5: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.6: 2024-01-17
  Changes: Refinement description