8BGL

Structure of the dimeric rsCherryRev1.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

An unusual disulfide-linked dimerization in the fluorescent protein rsCherryRev1.4.

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

(2023) Acta Crystallogr F Struct Biol Commun 79: 38-44

  • DOI: https://doi.org/10.1107/S2053230X23000572
  • Primary Citation of Related Structures:  
    8BGL

  • PubMed Abstract: 

    rsCherryRev1.4 has been reported as one of the reversibly photoswitchable variants of mCherry, and is an improved version with a faster off-switching speed and lower switching fatigue at high light intensities than its precursor rsCherryRev. However, rsCherryRev1.4 still has some limitations such as a tendency to dimerize as well as complex photophysical properties. Here, the crystal structure of rsCherryRev1.4 was determined at a resolution of 2 Å and it was discovered that it forms a dimer that shows disulfide bonding between the protomers. Mutagenesis, gel electrophoresis and size-exclusion chromatography strongly implicate Cys24 in this process. Replacing Cys24 in rsCherryRev1.4 resulted in a much lower tendency towards dimerization, while introducing Cys24 into mCherry correspondingly increased its dimerization. In principle, this finding opens the possibility of developing redox sensors based on controlled dimerization via disulfide cross-linking in fluorescent proteins, even though the actual application of engineering such sensors still requires additional research.


  • Organizational Affiliation

    Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rsCherryRev1.4
A, B
267Discosoma sp.Mutation(s): 37 
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, B
L-PEPTIDE LINKINGC9 H11 N3 O4 SMET, TYR, GLY
QYX
Query on QYX
A, B
L-PEPTIDE LINKINGC16 H18 N3 O4 SMET, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.104α = 90
b = 48.822β = 101.16
c = 99.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government911 project
KU LeuvenBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-04-05
    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