2GX2

Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of the photoswitchable fluorescent protein Dronpa-C62S

Nam, K.-H.Kwon, O.Y.Sugiyama, K.Lee, W.-H.Kim, Y.K.Song, H.K.Kim, E.E.Park, S.-Y.Jeon, H.Hwang, K.Y.

(2007) Biochem.Biophys.Res.Commun. 354: 962-967

  • DOI: 10.1016/j.bbrc.2007.01.086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The photoswitching behavior of green fluorescent proteins (GFPs) or GFP-like proteins is increasingly recognized as a new technique for optical marking. Recently, Ando and his colleagues developed a new green fluorescent protein Dronpa, which possess ...

    The photoswitching behavior of green fluorescent proteins (GFPs) or GFP-like proteins is increasingly recognized as a new technique for optical marking. Recently, Ando and his colleagues developed a new green fluorescent protein Dronpa, which possesses the unique photochromic property of being photoswitchable in a non-destructive manner. To better understand this mechanism, we determined the crystal structures of a new GFP Dronpa and its mutant C62S, at 1.9 Angstroms and 1.8 Angstroms, respectively. Determination of the structures demonstrates that a unique hydrogen-bonding network and the sulfur atom of the chromophore are critical to the photoswitching property of Dronpa. Reversible photoswitching was lost in cells expressing the Dronpa-C62S upon repetitive irradiation compared to the native protein. Structural and mutational analyses reveal the chemical basis for the functional properties of photoswitchable fluorescent proteins and provide the basis for subsequent coherent engineering of this subfamily of Dronpa homologs.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Anam-Dong, Sungbuk-Gu, Seoul, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
fluorescent protein Dronpa
A, B, C, D, E, F, G, H, I, J, K, L
243Echinophyllia sp. SC22Mutation(s): 0 
Gene Names: Dronpa
Find proteins for Q5TLG6 (Echinophyllia sp. SC22)
Go to UniProtKB:  Q5TLG6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYS
Query on GYS
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC14 H15 N3 O5SER, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 73.091α = 61.17
b = 106.160β = 70.85
c = 110.070γ = 86.21
Software Package:
Software NamePurpose
X-PLORphasing
CNSrefinement
ADSCdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance