9H25 | pdb_00009h25

Structure of rsCherry exposed to oxygen for 16 days

• PDB DOI: https://doi.org/10.2210/pdb9H25/pdb

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


• Deposited: 2024-10-11 Released: 2025-08-20 
• Deposition Author(s): Bui, T.Y.H., Van Meervelt, L.
• Funding Organization(s): KU Leuven

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure analysis of oxygen-induced degradation occurring in rsCherry.

Bui, T.Y.H., Pecqueur, L., Dedecker, P., Van Meervelt, L.

(2025) Acta Crystallogr F Struct Biol Commun 81: 311-318

• PubMed: 40552439 
• DOI: https://doi.org/10.1107/S2053230X25005485
• Primary Citation of Related Structures:  
  9H25, 9H26, 9H27, 9JX2


• PubMed Abstract: 
  

  rsCherry was one of the first reversibly photoswitchable variants to be developed from mCherry. However, its practical applications have been limited due to several inherent drawbacks. We have recently shown that the purified protein undergoes oxygen-induced chromophore degradation in solution, resulting in the progressive loss of its fluorescence and color. In this work, we present four crystal structures of rsCherry that exhibit varying degrees of degradation. Our structural analysis indicates that oxygen-induced degradation of rsCherry predominantly affects the chromophore without altering the protein backbone. Changes were only observed in the conformation of Lys70, confirming the crucial role of this residue in chromophore damage in rsCherry. Overall, this study provides valuable insights into the structural changes triggered by oxygen exposure in rsCherry, offering suggestions for the development of stable red fluorescent proteins with improved resistance to oxidative damage.

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Organizational Affiliation: 
• Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, Leuven, Belgium.
Chemistry of Biological Processes, Collège de France, Paris, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.16 kDa 
• Atom Count: 2,073 
• Modeled Residue Count: 221 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rsCherry	A	263	Discosoma sp.	Mutation(s): 32  Gene Names: PAmCherry, PAmCherry1
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8  Go to UniProtKB:  Q9U6Y8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
Q2K	A	L-PEPTIDE LINKING	C9 H11 N3 O4 S		MET, TYR, GLY
QIP	A	L-PEPTIDE LINKING	C9 H14 N4 O4 S		MET, TYR, GLY
QYX	A	L-PEPTIDE LINKING	C16 H18 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.391	α = 90
b = 43.452	β = 106
c = 108.818	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Bui, T.Y.H., Van Meervelt, L.

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Funding Organization	Location	Grant Number
KU Leuven	Belgium	--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release