8U52 | pdb_00008u52

Co-crystal structure of human transthyretin conjugated to the stilbene substructure derived from reaction with the fluorogenic covalent kinetic stabilizer A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The conformational landscape of human transthyretin revealed by cryo-EM.

Basanta, B.Nugroho, K.Yan, N.L.Kline, G.M.Powers, E.T.Tsai, F.J.Wu, M.Hansel-Harris, A.Chen, J.S.Forli, S.Kelly, J.W.Lander, G.C.

(2025) Nat Struct Mol Biol 32: 876-883

  • DOI: https://doi.org/10.1038/s41594-024-01472-7
  • Primary Citation of Related Structures:  
    8U52, 8VE0, 8VE1, 8VE2, 8VE3, 8VE4, 8VE5, 8VE6

  • PubMed Abstract: 

    Transthyretin (TTR) is a natively tetrameric thyroxine transporter in blood and cerebrospinal fluid whose misfolding and aggregation causes TTR amyloidosis. A rational drug design campaign identified the small molecule tafamidis (Vyndamax) as a stabilizer of the native TTR fold, and this aggregation inhibitor is regulatory agency approved for the treatment of TTR amyloidosis. Here we used cryo-EM to investigate the conformational landscape of this 55 kDa tetramer in the absence and presence of one or two ligands, revealing inherent asymmetries in the tetrameric architecture and previously unobserved conformational states. These findings provide critical mechanistic insights into negatively cooperative ligand binding and the structural pathways responsible for TTR amyloidogenesis, underscoring the capacity of cryo-EM to identify pharmacological targets suppressed by the confines of the crystal lattice, opening uncharted territory in structure-based drug design.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.

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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1W4 (Subject of Investigation/LOI)
Query on 1W4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
S-(4-fluorophenyl) 3-(dimethylamino)-5-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzenecarbothioate
C25 H24 F N O2 S
HDIQCNNYMZBHKA-AATRIKPKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.96α = 90
b = 85.201β = 90
c = 63.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States5R01DK046335-32

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references