6PFT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/jacs.9b08356
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Department of Physics , Stanford University , Stanford , California 94305 , United States.,Department of Chemistry , Stanford University , Stanford , California 94305 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
250Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OHD
Query on OHD
A
L-peptide linkingC14 H14 Cl N3 O4ALA,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.014α = 90.00
b = 62.716β = 90.00
c = 68.619γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118044

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references
  • Version 1.2: 2019-10-16
    Type: Data collection, Database references