2POX | pdb_00002pox

Dark state structure of the reversibly switchable fluorescent protein Dronpa

• PDB DOI: https://doi.org/10.2210/pdb2POX/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Echinophyllia sp. SC22
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-27 Released: 2007-07-17 
• Deposition Author(s): Trowitzsch, S., Weber, G., Wahl, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structural basis for reversible photoswitching in Dronpa

Andresen, M., Stiel, A.C., Trowitzsch, S., Weber, G., Eggeling, C., Wahl, M.C., Hell, S.W., Jakobs, S.

(2007) Proc Natl Acad Sci U S A 104: 13005-13009

• PubMed: 17646653 
• DOI: https://doi.org/10.1073/pnas.0700629104
• Primary Citation Related Structures: 
  2POX


• PubMed Abstract: 
  

  Dronpa is a novel GFP-like fluorescent protein with exceptional light-controlled switching properties. It may be reversibly switched between a fluorescent on-state and a nonfluorescent off-state by irradiation with light. To elucidate the molecular basis of the switching mechanism, we generated reversibly switchable Dronpa protein crystals. Using these crystals we determined the elusive dark-state structure of Dronpa at 1.95-A resolution. We found that the photoswitching results in a cis-trans isomerization of the chromophore accompanied by complex structural rearrangements of four nearby amino acid residues. Because of this cascade of intramolecular events, the chromophore is exposed to distinct electrostatic surface potentials, which are likely to influence the protonation equilibria at the chromophore. We suggest a comprehensive model for the light-induced switching mechanism, connecting a cascade of structural rearrangements with different protonation states of the chromophore.

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Organizational Affiliation: 
• Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.99 kDa 
• Atom Count: 8,450 
• Modeled Residue Count: 870 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescent protein Dronpa	A, B, C, D	255	Echinophyllia sp. SC22	Mutation(s): 1  Gene Names: Dronpa
UniProt
Find proteins for Q5TLG6 (Echinophyllia sp. SC22) Explore Q5TLG6  Go to UniProtKB:  Q5TLG6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYC	A, B, C, D	L-PEPTIDE LINKING	C14 H15 N3 O4 S		CYS, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.894	α = 90
b = 107.504	β = 90
c = 275.663	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Trowitzsch, S., Weber, G., Wahl, M.C.

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2007-09-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2020-04-15
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-30
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence