7ZBD

HaloTag with TRaQ-G ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A locally activatable sensor for robust quantification of organellar glutathione.

Emmert, S.Quargnali, G.Thallmair, S.Rivera-Fuentes, P.

(2023) Nat Chem 15: 1415-1421

  • DOI: https://doi.org/10.1038/s41557-023-01249-3
  • Primary Citation of Related Structures:  
    7ZBA, 7ZBB, 7ZBD

  • PubMed Abstract: 

    Glutathione (GSH) is the main determinant of intracellular redox potential and participates in multiple cellular signalling pathways. Achieving a detailed understanding of intracellular GSH homeostasis depends on the development of tools to map GSH compartmentalization and intra-organelle fluctuations. Here we present a GSH-sensing platform for live-cell imaging, termed targetable ratiometric quantitative GSH (TRaQ-G). This chemogenetic sensor possesses a unique reactivity turn-on mechanism, ensuring that the small molecule is only sensitive to GSH in a desired location. Furthermore, TRaQ-G can be fused to a fluorescent protein to give a ratiometric response. Using TRaQ-G fused to a redox-insensitive fluorescent protein, we demonstrate that the nuclear and cytosolic GSH pools are independently regulated during cell proliferation. This sensor was used in combination with a redox-sensitive fluorescent protein to quantify redox potential and GSH concentration simultaneously in the endoplasmic reticulum. Finally, by exchanging the fluorescent protein, we created a near-infrared, targetable and quantitative GSH sensor.


  • Organizational Affiliation

    Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéral de Lausanne, Lausanne, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase
A, B
303Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 20 
Gene Names: dhaA
EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp)
Explore P0A3G3 
Go to UniProtKB:  P0A3G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ILU (Subject of Investigation/LOI)
Query on ILU

Download Ideal Coordinates CCD File 
G [auth B][7-azanyl-10-[5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]-2-(cyanocarbamoyl)phenyl]-5,5-dimethyl-benzo[b][1]benzosilin-3-ylidene]-methyl-azanium
C35 H43 Cl N5 O4 Si
MOOPIZWXYFKFBC-JBFMKSPFSA-O
ILQ (Subject of Investigation/LOI)
Query on ILQ

Download Ideal Coordinates CCD File 
D [auth A](10R)-7-azanyl-N-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-2'-cyano-5,5-dimethyl-3-(methylamino)-1'-oxidanylidene-spiro[benzo[b][1]benzosiline-10,3'-isoindole]-5'-carboxamide
C35 H42 Cl N5 O4 Si
FJKIBVRSCRUAPC-PGUFJCEWSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.905α = 90
b = 50.46β = 117.74
c = 79.476γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPCEGP2_186862

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-07-19
    Changes: Database references, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references
  • Version 1.4: 2024-02-07
    Changes: Refinement description