5FHV | pdb_00005fhv

Crystal structure of mCherry after reaction with 2-mercaptoethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.188 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5FHV

This is version 2.0 of the entry. See complete history

Literature

Efficient switching of mCherry fluorescence using chemical caging.

Cloin, B.M.C.De Zitter, E.Salas, D.Gielen, V.Folkers, G.E.Mikhaylova, M.Bergeler, M.Krajnik, B.Harvey, J.Hoogenraad, C.C.Van Meervelt, L.Dedecker, P.Kapitein, L.C.

(2017) Proc Natl Acad Sci U S A 114: 7013-7018

  • DOI: https://doi.org/10.1073/pnas.1617280114
  • Primary Citation Related Structures: 
    5FHV

  • PubMed Abstract: 

    Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantum-mechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores.


  • Organizational Affiliation
    • Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 31.16 kDa 
  • Atom Count: 2,290 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 268 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mCherry-BME267Discosoma sp.Mutation(s): 0 
UniProt
Find proteins for D0VWW2 (Discosoma sp.)
Explore D0VWW2 
Go to UniProtKB:  D0VWW2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWW2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.188 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.783α = 90
b = 43.244β = 111.52
c = 61.234γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence, Structure summary