5CR1

Crystal structure of TTR/resveratrol/T4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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
  • Structures With Same Primary Citation

  • 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, rodolfo.berni@unipr.it.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TransthyretinA, B116Homo sapiensMutation(s): 1 
Gene Names: TTRPALB
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
NIH Common Fund Data Resources
PHAROS  P02766
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T44
Query on T44

Download CCD File 
A
3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-LBPRGKRZSA-N
 Ligand Interaction
STL
Query on STL

Download CCD File 
B
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T44IC50:  2200   nM  BindingDB
T44IC50:  2188   nM  BindingDB
T44IC50:  10500   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.536α = 90
b = 85.633β = 90
c = 63.826γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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