4YDN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1021/jacs.5b03042
  • Primary Citation of Related Structures:  
    4YDM, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
127Homo sapiensMutation(s): 0 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2WN
Query on 2WN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
4-[5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenyl sulfurofluoridate
C14 H7 Cl2 F N2 O5 S
RSJRYZBNJGGTGQ-UHFFFAOYSA-N
4B8
Query on 4B8

Download Ideal Coordinates CCD File 
D [auth A]2,6-dichloro-4-[5-(4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenol
C14 H8 Cl2 N2 O3
ZFNJTKVOZGKOOB-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4AK
Query on 4AK
A, B
L-PEPTIDE LINKINGC6 H14 N2 O5 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.093α = 90
b = 85.522β = 90
c = 64.65γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Advisory, Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description