2Z6X

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • R-Value Observed: 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 U S A 105: 9227-9232

  • DOI: 10.1073/pnas.0709599105
  • Primary Citation of Related Structures:  
    2Z6X, 2Z6Y, 2Z6Z, 2Z1O

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
photochromic protein DronpaABCDEFGH255PectiniidaeMutation(s): 0 
Find proteins for Q5TLG6 (Echinophyllia sp. SC22)
Explore Q5TLG6 
Go to UniProtKB:  Q5TLG6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYC
Query on GYC
A,B,C,D,E,F,G,HL-PEPTIDE LINKINGC14 H15 N3 O4 SCYS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.683α = 90
b = 111.683β = 90
c = 156.531γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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