2Z6X

Crystal structure of 22G, the wild-type protein of the photoswitchable GFP-like protein Dronpa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Light-dependent regulation of structural flexibility in a photochromic fluorescent protein.

Mizuno, H.Mal, T.K.Walchli, M.Kikuchi, A.Fukano, T.Ando, R.Jeyakanthan, J.Taka, J.Shiro, Y.Ikura, M.Miyawaki, A.

(2008) Proc.Natl.Acad.Sci.Usa 105: 9227-9232

  • DOI: 10.1073/pnas.0709599105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structural basis for the photochromism in the fluorescent protein Dronpa is poorly understood, because the crystal structures of the bright state of the protein did not provide an answer to the mechanism of the photochromism, and structural deter ...

    The structural basis for the photochromism in the fluorescent protein Dronpa is poorly understood, because the crystal structures of the bright state of the protein did not provide an answer to the mechanism of the photochromism, and structural determination of the dark state has been elusive. We performed NMR analyses of Dronpa in solution at ambient temperatures to find structural flexibility of the protein in the dark state. Light-induced changes in interactions between the chromophore and beta-barrel are responsible for switching between the two states. In the bright state, the apex of the chromophore tethers to the barrel by a hydrogen bond, and an imidazole ring protruding from the barrel stabilizes the plane of the chromophore. These interactions are disrupted by strong illumination with blue light, and the chromophore, together with a part of the beta-barrel, becomes flexible, leading to a nonradiative decay process.


    Organizational Affiliation

    Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-City, Saitama 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
photochromic protein Dronpa
A, B, C, D, E, F, G, H
257Echinophyllia sp. SC22Mutation(s): 0 
Gene Names: Dronpa
Find proteins for Q5TLG6 (Echinophyllia sp. SC22)
Go to UniProtKB:  Q5TLG6
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYC
Query on GYC
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC14 H15 N3 O4 SCYS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 111.683α = 90.00
b = 111.683β = 90.00
c = 156.531γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance