5CR1

Crystal structure of TTR/resveratrol/T4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.545 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Transthyretin Binding Heterogeneity and Anti-amyloidogenic Activity of Natural Polyphenols and Their Metabolites.

Florio, P.Folli, C.Cianci, M.Del Rio, D.Zanotti, G.Berni, R.

(2015) J.Biol.Chem. 290: 29769-29780

  • DOI: 10.1074/jbc.M115.690172
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transthyretin (TTR) is an amyloidogenic protein, the amyloidogenic potential of which is enhanced by a number of specific point mutations. The ability to inhibit TTR fibrillogenesis is known for several classes of compounds, including natural polyphe ...

    Transthyretin (TTR) is an amyloidogenic protein, the amyloidogenic potential of which is enhanced by a number of specific point mutations. The ability to inhibit TTR fibrillogenesis is known for several classes of compounds, including natural polyphenols, which protect the native state of TTR by specifically interacting with its thyroxine binding sites. Comparative analyses of the interaction and of the ability to protect the TTR native state for polyphenols, both stilbenoids and flavonoids, and some of their main metabolites have been carried out. A main finding of this investigation was the highly preferential binding of resveratrol and thyroxine, both characterized by negative binding cooperativity, to distinct sites in TTR, consistent with the data of x-ray analysis of TTR in complex with both ligands. Although revealing the ability of the two thyroxine binding sites of TTR to discriminate between different ligands, this feature has allowed us to evaluate the interactions of polyphenols with both resveratrol and thyroxine preferential binding sites, by using resveratrol and radiolabeled T4 as probes. Among flavonoids, genistein and apigenin were able to effectively displace resveratrol from its preferential binding site, whereas genistein also showed the ability to interact, albeit weakly, with the preferential thyroxine binding site. Several glucuronidated polyphenol metabolites did not exhibit significant competition for resveratrol and thyroxine preferential binding sites and lacked the ability to stabilize TTR. However, resveratrol-3-O-sulfate was able to significantly protect the protein native state. A rationale for the in vitro properties found for polyphenol metabolites was provided by x-ray analysis of their complexes with TTR.


    Organizational Affiliation

    From the Department of Life Sciences, University of Parma, 43124 Parma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
116Homo sapiensMutation(s): 0 
Gene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STL
Query on STL

Download SDF File 
Download CCD File 
B
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
 Ligand Interaction
T44
Query on T44

Download SDF File 
Download CCD File 
A
3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-LBPRGKRZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T44IC50: 2188 - 10500 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.545 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.536α = 90.00
b = 85.633β = 90.00
c = 63.826γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2015-12-23
    Type: Database references