6FFT

Neutron structure of human transthyretin (TTR) S52P mutant in complex with tafamidis at room temperature to 2A resolution (quasi-Laue)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.161 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A molecular mechanism for transthyretin amyloidogenesis.

Yee, A.W.Aldeghi, M.Blakeley, M.P.Ostermann, A.Mas, P.J.Moulin, M.de Sanctis, D.Bowler, M.W.Mueller-Dieckmann, C.Mitchell, E.P.Haertlein, M.de Groot, B.L.Boeri Erba, E.Forsyth, V.T.

(2019) Nat Commun 10: 925-925

  • DOI: 10.1038/s41467-019-08609-z
  • Primary Citation of Related Structures:  
    6FFT, 5NFE, 5NFW

  • PubMed Abstract: 
  • Human transthyretin (TTR) is implicated in several fatal forms of amyloidosis. Many mutations of TTR have been identified; most of these are pathogenic, but some offer protective effects. The molecular basis underlying the vastly different fibrillation behaviours of these TTR mutants is poorly understood ...

    Human transthyretin (TTR) is implicated in several fatal forms of amyloidosis. Many mutations of TTR have been identified; most of these are pathogenic, but some offer protective effects. The molecular basis underlying the vastly different fibrillation behaviours of these TTR mutants is poorly understood. Here, on the basis of neutron crystallography, native mass spectrometry and modelling studies, we propose a mechanism whereby TTR can form amyloid fibrils via a parallel equilibrium of partially unfolded species that proceeds in favour of the amyloidogenic forms of TTR. It is suggested that unfolding events within the TTR monomer originate at the C-D loop of the protein, and that destabilising mutations in this region enhance the rate of TTR fibrillation. Furthermore, it is proposed that the binding of small molecule drugs to TTR stabilises non-amyloidogenic states of TTR in a manner similar to that occurring for the protective mutants of the protein.


    Organizational Affiliation

    Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France. tforsyth@ill.eu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransthyretinA, B130Homo sapiensMutation(s): 1 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3MI (Subject of Investigation/LOI)
Query on 3MI

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid
C14 H7 Cl2 N O3
TXEIIPDJKFWEEC-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3MI BindingDB:  6FFT Kd: min: 4.4, max: 2800 (nM) from 7 assay(s)
IC50: min: 1550, max: 3100 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 2
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.901α = 90
b = 85.703β = 90
c = 65.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
LAUEGENdata reduction
XDSdata reduction
LSCALEdata scaling
SCALAdata scaling
REFMACphasing
Cootmodel building

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/C015452/1
Engineering and Physical Sciences Research CouncilUnited KingdomGR/R99393/01

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references