3W1D

Structure of a pressure sensitive YFP variant YFP-G3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glycine insertion makes yellow fluorescent protein sensitive to hydrostatic pressure.

Watanabe, T.M.Imada, K.Yoshizawa, K.Nishiyama, M.Kato, C.Abe, F.Morikawa, T.J.Kinoshita, M.Fujita, H.Yanagida, T.

(2013) Plos One 8: e73212-e73212

  • DOI: 10.1371/journal.pone.0073212
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fluorescent protein-based indicators for intracellular environment conditions such as pH and ion concentrations are commonly used to study the status and dynamics of living cells. Despite being an important factor in many biological processes, the de ...

    Fluorescent protein-based indicators for intracellular environment conditions such as pH and ion concentrations are commonly used to study the status and dynamics of living cells. Despite being an important factor in many biological processes, the development of an indicator for the physicochemical state of water, such as pressure, viscosity and temperature, however, has been neglected. We here found a novel mutation that dramatically enhances the pressure dependency of the yellow fluorescent protein (YFP) by inserting several glycines into it. The crystal structure of the mutant showed that the tyrosine near the chromophore flipped toward the outside of the β-can structure, resulting in the entry of a few water molecules near the chromophore. In response to changes in hydrostatic pressure, a spectrum shift and an intensity change of the fluorescence were observed. By measuring the fluorescence of the YFP mutant, we succeeded in measuring the intracellular pressure change in living cell. This study shows a new strategy of design to engineer fluorescent protein indicators to sense hydrostatic pressure.


    Organizational Affiliation

    RIKEN Quantitative Biology Center (QBiC), Suita, Osaka, Japan ; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan ; WPI, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan ; Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green Fluorescent protein
A
241Aequorea victoriaMutation(s): 4 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
A
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.050α = 90.00
b = 62.980β = 90.00
c = 70.020γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction
SPring-8data collection
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release