6D39 | pdb_00006d39

Photodissociable dimeric Dronpa green fluorescent protein variant V (pdDronpaV)

• PDB DOI: https://doi.org/10.2210/pdb6D39/pdb

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


• Deposited: 2018-04-15 Released: 2018-05-23 
• Deposition Author(s): Zhou, X., Fan, L., Lin, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.247 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Optical control of cell signaling by single-chain photoswitchable kinases.

Zhou, X.X., Fan, L.Z., Li, P., Shen, K., Lin, M.Z.

(2017) Science 355: 836-842

• PubMed: 28232577 
• DOI: https://doi.org/10.1126/science.aah3605
• Primary Citation Related Structures: 
  6D38, 6D39


• PubMed Abstract: 
  

  Protein kinases transduce signals to regulate a wide array of cellular functions in eukaryotes. A generalizable method for optical control of kinases would enable fine spatiotemporal interrogation or manipulation of these various functions. We report the design and application of single-chain cofactor-free kinases with photoswitchable activity. We engineered a dimeric protein, pdDronpa, that dissociates in cyan light and reassociates in violet light. Attaching two pdDronpa domains at rationally selected locations in the kinase domain, we created the photoswitchable kinases psRaf1, psMEK1, psMEK2, and psCDK5. Using these photoswitchable kinases, we established an all-optical cell-based assay for screening inhibitors, uncovered a direct and rapid inhibitory feedback loop from ERK to MEK1, and mediated developmental changes and synaptic vesicle transport in vivo using light.

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Organizational Affiliation: 
• Department of Bioengineering, Stanford University, Stanford, CA, USA.
Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA. [e-mail].
Department of Neurobiology, Stanford University, Stanford, CA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.93 kDa 
• Atom Count: 1,732 
• Modeled Residue Count: 213 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescent protein Dronpa	A	259	Echinophyllia sp. SC22	Mutation(s): 5  Gene Names: Dronpa
UniProt
Find proteins for Q5TLG6 (Echinophyllia sp. SC22) Explore Q5TLG6  Go to UniProtKB:  Q5TLG6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.247 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.917	α = 90
b = 51.917	β = 90
c = 163.581	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Zhou, X., Fan, L., Lin, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5DP1GM111003

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: 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