8VE5 | pdb_00008ve5

(Biarylamine-FT2-WT)1(C10A)3-human transthyretin in the compressed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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, C, D
144Homo 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
P2C (Subject of Investigation/LOI)
Query on P2C

Download Ideal Coordinates CCD File 
E [auth B]2-[(3,5-DICHLORO-4-TRIOXIDANYLPHENYL)AMINO]BENZOIC ACID
C13 H9 Cl2 N O5
SNAMTVTZDPUVRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM142196
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAG067594

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-05-28
    Changes: Data collection, Database references