6PFT | pdb_00006pft

rsEGFP2 with a chlorinated chromophore in the non-fluorescent off-state

• PDB DOI: https://doi.org/10.2210/pdb6PFT/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-22 Released: 2019-08-07 
• Deposition Author(s): Chang, J., Romei, M.G., Boxer, S.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.176 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins.

Chang, J., Romei, M.G., Boxer, S.G.

(2019) J Am Chem Soc 141: 15504-15508

• PubMed: 31533429 
• DOI: https://doi.org/10.1021/jacs.9b08356
• Primary Citation Related Structures: 
  6PFR, 6PFS, 6PFT, 6PFU


• PubMed Abstract: 
  

  Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of cis and trans rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the trans state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas, in a tighter packing (7% smaller unit cell size), the hula-twist occurs.

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Organizational Affiliation: 
• Department of Physics , Stanford University , Stanford , California 94305 , United States.
Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 28.66 kDa 
• Atom Count: 2,316 
• Modeled Residue Count: 241 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	250	Aequorea victoria	Mutation(s): 0
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OHD	A	L-PEPTIDE LINKING	C14 H14 Cl N3 O4		ALA, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.176 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.014	α = 90
b = 62.716	β = 90
c = 68.619	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Chang, J., Romei, M.G., Boxer, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118044

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection, Database references
• Version 2.0: 2020-01-01
  Changes: Author supporting evidence, Polymer sequence, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2023-11-15
  Changes: Data collection
• Version 3.0: 2026-03-18
  Changes: Polymer sequence, Structure summary