1H6R | pdb_00001h6r

The oxidized state of a redox sensitive variant of green fluorescent protein

• PDB DOI: https://doi.org/10.2210/pdb1H6R/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-06-22 Released: 2001-11-15 
• Deposition Author(s): Ostergaard, H., Henriksen, A., Hansen, F.G., Winther, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.212 (Depositor) 
• R-Value Work: 
  0.183 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Shedding Light on Disulfide Bond Formation: Engineering a Redox Switch in Green Fluorescent Protein

Ostergaard, H., Henriksen, A., Hansen, F.G., Winther, J.R.

(2001) EMBO J 20: 5853

• PubMed: 11689426 
• DOI: https://doi.org/10.1093/emboj/20.21.5853
• Primary Citation Related Structures: 
  1H6R


• PubMed Abstract: 
  

  To visualize the formation of disulfide bonds in living cells, a pair of redox-active cysteines was introduced into the yellow fluorescent variant of green fluorescent protein. Formation of a disulfide bond between the two cysteines was fully reversible and resulted in a >2-fold decrease in the intrinsic fluorescence. Inter conversion between the two redox states could thus be followed in vitro as well as in vivo by non-invasive fluorimetric measurements. The 1.5 A crystal structure of the oxidized protein revealed a disulfide bond-induced distortion of the beta-barrel, as well as a structural reorganization of residues in the immediate chromophore environment. By combining this information with spectroscopic data, we propose a detailed mechanism accounting for the observed redox state-dependent fluorescence. The redox potential of the cysteine couple was found to be within the physiological range for redox-active cysteines. In the cytoplasm of Escherichia coli, the protein was a sensitive probe for the redox changes that occur upon disruption of the thioredoxin reductive pathway.

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Organizational Affiliation: 
• Section of Molecular Microbiology, BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Lyngby, Denmark.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 80.9 kDa 
• Atom Count: 6,447 
• Modeled Residue Count: 687 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GREEN FLUORESCENT PROTEIN	A, B, C	236	Aequorea victoria	Mutation(s): 9
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.212 (Depositor) 
• R-Value Work:  0.183 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.864	α = 90
b = 93.915	β = 90
c = 140.551	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-15 
Deposition Author(s): Ostergaard, H., Henriksen, A., Hansen, F.G., Winther, J.R.

Revision History  

• Version 1.0: 2001-11-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2019-10-23
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description