8B7G

Structure of oxygen-degraded rsCherry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry.

Bui, T.Y.H.De Zitter, E.Moeyaert, B.Pecqueur, L.Srinivasu, B.Y.Economou, A.Fontecave, M.Van Meervelt, L.Dedecker, P.Pedre, B.

(2023) Int J Biol Macromol 239: 124179-124179

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.124179
  • Primary Citation of Related Structures:  
    8B65, 8B7G

  • PubMed Abstract: 

    Reversibly switchable monomeric Cherry (rsCherry) is a photoswitchable variant of the red fluorescent protein mCherry. We report that this protein gradually and irreversibly loses its red fluorescence in the dark over a period of months at 4 °C and a few days at 37 °C. We also find that its ancestor, mCherry, undergoes a similar fluorescence loss but at a slower rate. X-ray crystallography and mass spectrometry reveal that this is caused by the cleavage of the p-hydroxyphenyl ring from the chromophore and the formation of two novel types of cyclic structures at the remaining chromophore moiety. Overall, our work sheds light on a new process occurring within fluorescent proteins, further adding to the chemical diversity and versatility of these molecules.


  • Organizational Affiliation

    Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rsCherry269Discosoma sp.Mutation(s): 32 
UniProt
Find proteins for D1MPT3 (Discosoma sp.)
Explore D1MPT3 
Go to UniProtKB:  D1MPT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1MPT3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
Q2K
Query on Q2K
A
L-PEPTIDE LINKINGC9 H11 N3 O4 SMET, TYR, GLY
QIP
Query on QIP
A
L-PEPTIDE LINKINGC9 H14 N4 O4 SMET, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.213α = 90
b = 43.177β = 106.06
c = 108.529γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentViet Nam911 project
KU LeuvenBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-04-19
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-02-07
    Changes: Refinement description