6GOO

Crystal Structure Of Sea Bream Transthyretin in complex with Perfluorooctanoic acid (PFOA). Crystallized in AmSO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interspecies Variation Between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals.

Zhang, J.Grundstrom, C.Brannstrom, K.Iakovleva, I.Lindberg, M.Olofsson, A.Andersson, P.L.Sauer-Eriksson, A.E.

(2018) Environ. Sci. Technol. --: --

  • DOI: 10.1021/acs.est.8b03581
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone hom ...

    Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone homeostasis. Transthyretin (TTR) is found in serum and cerebrospinal fluid of vertebrates, where it transports thyroid hormones. Here we explored the interspecies variation in TDC binding to human and fish TTR (exemplified by Gilthead seabream (Sparus aurata)). The in vitro binding experiments showed that TDCs bind with equal or weaker affinity to seabream TTR than to the human TTR, particular, the polar TDCs (>500-fold lower affinity). Crystal structures of seabream TTR-TDC complexes revealed that all TDCs bound at the thyroid binding sites. However, amino acid substitution of Ser117 in human TTR to Thr117 in seabream prevented polar TDCs from binding deep in the hormone binding cavity, which explains their low affinity to seabream TTR. Molecular dynamics and in silico alanine scanning simulation also suggested that the protein backbone of seabream TTR is more rigid than the human one and that Thr117 provides fewer electrostatic contributions than Ser117 to ligand bindings. This provides an explanation for the weaker affinities of the ligands that rely on electrostatic interactions with Thr117. The lower affinities of TDCs to fish TTR, in particular the polar ones, could potentially lead to milder thyroid-related effects in fish.


    Related Citations: 
    • Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.
      Zhang, J.,Begum, A.,Brannstrom, K.,Grundstrom, C.,Iakovleva, I.,Olofsson, A.,Sauer-Eriksson, A.E.,Andersson, P.L.
      (2016) Environ. Sci. Technol. 50: 11984



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
135Sparus aurataMutation(s): 0 
Find proteins for Q9PTT3 (Sparus aurata)
Go to UniProtKB:  Q9PTT3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8PF
Query on 8PF

Download SDF File 
Download CCD File 
A, B
pentadecafluorooctanoic acid
C8 H F15 O2
SNGREZUHAYWORS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.608α = 90.00
b = 59.608β = 90.00
c = 116.040γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references
  • Version 1.2: 2018-09-26
    Type: Data collection, Database references