6VIO

Crystal structure of eYFP His148Ser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering

Peng, B.Dikdan, R.Hill, S.E.Patterson-Orazem, A.C.Lieberman, R.L.Fahrni, C.J.Dickson, R.M.

(2021) J Phys Chem B 125: 5200-5209

  • DOI: https://doi.org/10.1021/acs.jpcb.1c00649
  • Primary Citation of Related Structures:  
    6VIO

  • PubMed Abstract: 

    Modulating fluorescent protein emission holds great potential for increasing readout sensitivity for applications in biological imaging and detection. Here, we identify and engineer optically modulated yellow fluorescent proteins (EYFP, originally 10C, but renamed EYFP later, and mVenus) to yield new emitters with distinct modulation profiles and unique, optically gated, delayed fluorescence. The parent YFPs are individually modulatable through secondary illumination, depopulating a long-lived dark state to dynamically increase fluorescence. A single point mutation introduced near the chromophore in each of these YFPs provides access to a second, even longer-lived modulatable dark state, while a different double mutant renders EYFP unmodulatable. The naturally occurring dark state in the parent YFPs yields strong fluorescence modulation upon long-wavelength-induced dark state depopulation, allowing selective detection at the frequency at which the long wavelength secondary laser is intensity modulated. Distinct from photoswitches, however, this near IR secondary coexcitation repumps the emissive S 1 level from the long-lived triplet state, resulting in optically activated delayed fluorescence (OADF). This OADF results from secondary laser-induced, reverse intersystem crossing (RISC), producing additional nanosecond-lived, visible fluorescence that is delayed by many microseconds after the primary excitation has turned off. Mutation of the parent chromophore environment opens an additional modulation pathway that avoids the OADF-producing triplet state, resulting in a second, much longer-lived, modulatable dark state. These Optically Modulated and Optically Activated Delayed Fluorescent Proteins (OMFPs and OADFPs) are thus excellent for background- and reference-free, high sensitivity cellular imaging, but time-gated OADF offers a second modality for true background-free detection. Our combined structural and spectroscopic data not only gives additional mechanistic details for designing optically modulated fluorescent proteins but also provides the opportunity to distinguish similarly emitting OMFPs through OADF and through their unique modulation spectra.


  • Organizational Affiliation

    School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein GFP
A, B, C, D, E
A, B, C, D, E, F, G, H
260Aequorea victoriaMutation(s): 2 
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42212
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CR2
Query on CR2
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.651α = 85.12
b = 56.772β = 85.26
c = 148.193γ = 70.48
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR01EY021205

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection