3NG5

Crystal Structure of V30M transthyretin complexed with (-)-epigallocatechin gallate (EGCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of green tea polyphenol(-)-epigallocatechin gallate (EGCG)-transthyretin complex reveals novel binding site distinct from thyroxine binding site

Miyata, M.Sato, T.Kugimiya, M.Sho, M.Nakamura, T.Ikemizu, S.Chirifu, M.Mizuguchi, M.Nabeshima, Y.Suwa, Y.Morioka, H.Arimori, T.Suico, M.A.Shuto, T.Sako, Y.Momohara, M.Koga, T.Morino-Koga, S.Yamagata, Y.Kai, H.

(2010) Biochemistry --: --

  • DOI: 10.1021/bi1004409

  • PubMed Abstract: 
  • Amyloid fibril formation is associated with protein misfolding disorders, including neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases. Familial amyloid polyneuropathy (FAP) is a hereditary disease caused by a poin ...

    Amyloid fibril formation is associated with protein misfolding disorders, including neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases. Familial amyloid polyneuropathy (FAP) is a hereditary disease caused by a point mutation of the human plasma protein, transthyretin (TTR), which binds and transports thyroxine (T(4)). TTR variants contribute to the pathogenesis of amyloidosis by forming amyloid fibrils in the extracellular environment. A recent report showed that epigallocatechin 3-gallate (EGCG), the major polyphenol component of green tea, binds to TTR and suppresses TTR amyloid fibril formation. However, structural analysis of EGCG binding to TTR has not yet been conducted. Here we first investigated the crystal structure of the EGCG-V30M TTR complex and found novel binding sites distinct from the thyroxine binding site, suggesting that EGCG has a mode of action different from those of previous chemical compounds that were shown to bind and stabilize the TTR tetramer structure. Furthermore, EGCG induced the oligomerization and monomer suppression in the cellular system of clinically reported TTR variants. Taken together, these findings suggest the possibility that EGCG may be a candidate compound for FAP therapy.


    Organizational Affiliation

    Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensMutations: V30M
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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
KDH
Query on KDH

Download SDF File 
Download CCD File 
A, B
(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate
(-)-Epigallocatechin-3-gallate, EGCG
C22 H18 O11
WMBWREPUVVBILR-WIYYLYMNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.074α = 90.00
b = 44.189β = 90.00
c = 65.141γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
ADSCdata collection
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance