4YDM

High resolution crystal structure of human transthyretin bound to ligand and conjugates of 3-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl)phenyl fluorosulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Fluorogenic Aryl Fluorosulfate for Intraorganellar Transthyretin Imaging in Living Cells and in Caenorhabditis elegans.

Baranczak, A.Liu, Y.Connelly, S.Du, W.G.Greiner, E.R.Genereux, J.C.Wiseman, R.L.Eisele, Y.S.Bradbury, N.C.Dong, J.Noodleman, L.Sharpless, K.B.Wilson, I.A.Encalada, S.E.Kelly, J.W.

(2015) J.Am.Chem.Soc. 137: 7404-7414

  • DOI: 10.1021/jacs.5b03042
  • Primary Citation of Related Structures:  4YDN

  • PubMed Abstract: 
  • Fluorogenic probes, due to their often greater spatial and temporal sensitivity in comparison to permanently fluorescent small molecules, represent powerful tools to study protein localization and function in the context of living systems. Herein, we ...

    Fluorogenic probes, due to their often greater spatial and temporal sensitivity in comparison to permanently fluorescent small molecules, represent powerful tools to study protein localization and function in the context of living systems. Herein, we report fluorogenic probe 4, a 1,3,4-oxadiazole designed to bind selectively to transthyretin (TTR). Probe 4 comprises a fluorosulfate group not previously used in an environment-sensitive fluorophore. The fluorosulfate functional group does not react covalently with TTR on the time scale required for cellular imaging, but does red shift the emission maximum of probe 4 in comparison to its nonfluorosulfated analogue. We demonstrate that probe 4 is dark in aqueous buffers, whereas the TTR·4 complex exhibits a fluorescence emission maximum at 481 nm. The addition of probe 4 to living HEK293T cells allows efficient binding to and imaging of exogenous TTR within intracellular organelles, including the mitochondria and the endoplasmic reticulum. Furthermore, live Caenorhabditis elegans expressing human TTR transgenically and treated with probe 4 display TTR·4 fluorescence in macrophage-like coelomocytes. An analogue of fluorosulfate probe 4 does react selectively with TTR without labeling the remainder of the cellular proteome. Studies on this analogue suggest that certain aryl fluorosulfates, due to their cell and organelle permeability and activatable reactivity, could be considered for the development of protein-selective covalent probes.


    Organizational Affiliation

    †Department of Chemistry, ‡Department of Molecular and Experimental Medicine, §Department of Integrative Structural and Computational Biology, ∥Department of Chemical Physiology, ⊥Department of Molecular and Cellular Neuroscience, #The Skaggs Institute for Chemical Biology, ∇Dorris Neuroscience Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4AJ
Query on 4AJ

Download SDF File 
Download CCD File 
A, B
2,6-dichloro-4-[5-(3-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenol
C14 H8 Cl2 N2 O3
XNFPUJQYKUISED-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4AK
Query on 4AK
A, B
L-peptide linkingC6 H14 N2 O5 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.709α = 90.00
b = 85.420β = 90.00
c = 63.537γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy