2IOV | pdb_00002iov

Bright-state structure of the reversibly switchable fluorescent protein Dronpa

• PDB DOI: https://doi.org/10.2210/pdb2IOV/pdb

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


• Deposited: 2006-10-11 Released: 2006-12-05 
• Deposition Author(s): Stiel, A.C., Trowitzsch, S., Weber, G., Andresen, M., Eggeling, C., Hell, S.W., Jakobs, S., Wahl, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.216 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants

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

(2007) Biochem J 402: 35-42

• PubMed: 17117927 
• DOI: https://doi.org/10.1042/BJ20061401
• Primary Citation Related Structures: 
  2IOV


• PubMed Abstract: 
  

  RSFPs (reversibly switchable fluorescent proteins) may be repeatedly converted between a fluorescent and a non-fluorescent state by irradiation and have attracted widespread interest for many new applications. The RSFP Dronpa may be switched with blue light from a fluorescent state into a non-fluorescent state, and back again with UV light. To obtain insight into the underlying molecular mechanism of this switching, we have determined the crystal structure of the fluorescent equilibrium state of Dronpa. Its bicyclic chromophore is formed spontaneously from the Cys62-Tyr63-Gly64 tripeptide. In the fluorescent state, it adopts a slightly non-coplanar cis conformation within the interior of a typical GFP (green fluorescent protein) b-can fold. Dronpa shares some structural features with asFP595, another RSFP whose chromophore has previously been demonstrated to undergo a cis-trans isomerization upon photoswitching. Based on the structural comparison with asFP595, we have generated new Dronpa variants with an up to more than 1000-fold accelerated switching behaviour. The mutations which were introduced at position Val157 or Met159 apparently reduce the steric hindrance for a cis-trans isomerization of the chromophore, thus lowering the energy barrier for the blue light-driven on-to-off transition. The findings reported in the present study support the view that a cis-trans isomerization is one of the key events common to the switching mechanism in RSFPs.

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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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.99 kDa 
• Atom Count: 8,339 
• Modeled Residue Count: 875 
• 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: 1.80 Å
• R-Value Free:  0.216 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.292	α = 90
b = 109.627	β = 90
c = 275.232	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Stiel, A.C., Trowitzsch, S., Weber, G., Andresen, M., Eggeling, C., Hell, S.W., Jakobs, S., Wahl, M.C.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-16
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence