4I89

Crystal structure of transthyretin in complex with diflunisal at acidic pH

• PDB DOI: https://doi.org/10.2210/pdb4I89/pdb

• Classification: transport protein/inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-12-03 Released: 2013-06-19 
• Deposition Author(s): Zanotti, G., Cendron, L., Folli, C., Florio, P., Imbimbo, B.P., Berni, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Structural evidence for native state stabilization of a conformationally labile amyloidogenic transthyretin variant by fibrillogenesis inhibitors.

Zanotti, G., Cendron, L., Folli, C., Florio, P., Imbimbo, B.P., Berni, R.

(2013) FEBS Lett 587: 2325-2331

• PubMed: 23792159 
• DOI: https://doi.org/10.1016/j.febslet.2013.06.016
• Primary Citation of Related Structures:  
  4I85, 4I87, 4I89


• PubMed Abstract: 
  

  Several classes of chemicals are able to bind to the thyroxine binding sites of transthyretin (TTR), stabilizing its native state and inhibiting in vitro the amyloidogenic process. The amyloidogenic I84S TTR variant undergoes a large conformational change at moderately acidic pH. Structural evidence has been obtained by X-ray analysis for the native state stabilization of I84S TTR by two chemically distinct fibrillogenesis inhibitors. In fact, they fully prevent the acidic pH-induced protein conformational change as a result of a long-range stabilizing effect. This study provides further support to the therapeutic strategy based on the use of TTR stabilizers as anti-amyloidogenic drugs.

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Organizational Affiliation: 

Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28 kDa 
• Atom Count: 2,081 
• Modelled Residue Count: 231 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	127	Homo sapiens	Mutation(s): 1  Gene Names: PALB, TTR
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens) Explore P02766  Go to UniProtKB:  P02766
PHAROS:  P02766 GTEx:  ENSG00000118271

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FL	C [auth A], D [auth B]	5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID C13 H8 F2 O3 HUPFGZXOMWLGNK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.8	α = 90
b = 86.22	β = 90
c = 64.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Zanotti, G., Cendron, L., Folli, C., Florio, P., Imbimbo, B.P., Berni, R.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2013-08-07
  Changes: Non-polymer description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description