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 8B7G | pdb_00008b7g

Structure of oxygen-degraded rsCherry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.146 (Depositor), 0.147 (DCC) 
  • R-Value Work: 
    0.125 (Depositor), 0.126 (DCC) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8B7G

This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 31.27 kDa 
  • Atom Count: 2,376 
  • Modeled Residue Count: 220 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
rsCherry269Discosoma sp.Mutation(s): 32 
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.)
Explore Q9U6Y8 
Go to UniProtKB:  Q9U6Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6Y8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Non-standard Monomers  2 Unique
IDChains TypeFormula2D Diagram
Q2K
Query on Q2K
L-PEPTIDE LINKINGC9 H11 N3 O4 S
QIP
Query on QIP
L-PEPTIDE LINKINGC9 H14 N4 O4 S

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.146 (Depositor), 0.147 (DCC) 
  • R-Value Work:  0.125 (Depositor), 0.126 (DCC) 
  • R-Value Observed: 0.126 (Depositor) 
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
  • Version 2.2: 2024-11-13
    Changes: Structure summary