5N5Q

Human TTR altered conformation from soaking in iron chloride.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Copper mediated amyloid-beta binding to Transthyretin.

Ciccone, L.Fruchart-Gaillard, C.Mourier, G.Savko, M.Nencetti, S.Orlandini, E.Servent, D.Stura, E.A.Shepard, W.

(2018) Sci Rep 8: 13744-13744

  • DOI: https://doi.org/10.1038/s41598-018-31808-5
  • Primary Citation of Related Structures:  
    5N5Q, 5N62, 5N7C

  • PubMed Abstract: 

    Transthyretin (TTR), a homotetrameric protein that transports thyroxine and retinol both in plasma and in cerebrospinal (CSF) fluid provides a natural protective response against Alzheimer's disease (AD), modulates amyloid-β (Aβ) deposition by direct interaction and co-localizes with Aβ in plaques. TTR levels are lower in the CSF of AD patients. Zn 2+ , Mn 2+ and Fe 2+ transform TTR into a protease able to cleave Aβ. To explain these activities, monomer dissociation or conformational changes have been suggested. Here, we report that when TTR crystals are exposed to copper or iron salts, the tetramer undergoes a significant conformational change that alters the dimer-dimer interface and rearranges residues implicated in TTR's ability to neutralize Aβ. We also describe the conformational changes in TTR upon the binding of the various metal ions. Furthermore, using bio-layer interferometry (BLI) with immobilized Aβ(1-28), we observe the binding of TTR only in the presence of copper. Such Cu 2+ -dependent binding suggests a recognition mechanism whereby Cu 2+ modulates both the TTR conformation, induces a complementary Aβ structure and may participate in the interaction. Cu 2+ -soaked TTR crystals show a conformation different from that induced by Fe 2+ , and intriguingly, TTR crystals grown in presence of Aβ(1-28) show different positions for the copper sites from those grown its absence.


  • Organizational Affiliation

    CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
116Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FFE
Query on FFE

Download Ideal Coordinates CCD File 
D [auth A][bis(oxidanyl)-[tetrakis(oxidanyl)ferriooxy]ferrio]oxy-pentakis(oxidanyl)iron
Fe3 H11 O13
WDCOXZGBZIBJBW-UHFFFAOYSA-C
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B],
G [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.73α = 90
b = 81.81β = 90
c = 69.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description