1SN2 | pdb_00001sn2

Crystal Structure of Sea Bream Transthyretin at 1.90A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.210 (Depositor) 
  • R-Value Work: 
    0.175 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1SN2

This is version 1.4 of the entry. See complete history

Literature

High resolution crystal structures of piscine transthyretin reveal different binding modes for triiodothyronine and thyroxine.

Eneqvist, T.Lundberg, E.Karlsson, A.Huang, S.Santos, C.R.Power, D.M.Sauer-Eriksson, A.E.

(2004) J Biological Chem 279: 26411-26416

  • DOI: https://doi.org/10.1074/jbc.M313553200
  • Primary Citation Related Structures: 
    1SN0, 1SN2, 1SN5

  • PubMed Abstract: 

    Transthyretin (TTR) is an extracellular transport protein involved in the distribution of thyroid hormones and vitamin A. So far, TTR has only been found in vertebrates, of which piscine TTR displays the lowest sequence identity with human TTR (47%). Human and piscine TTR bind both thyroid hormones 3,5,3'-triiodo-l-thyronine (T(3)) and 3,5,3',5'-tetraiodo-l-thyronine (thyroxine, T(4)). Human TTR has higher affinity for T(4) than T(3), whereas the reverse holds for piscine TTR. X-ray structures of Sparus aurata (sea bream) TTR have been determined as the apo-protein at 1.75 A resolution and bound to ligands T(3) and T(4), both at 1.9 A resolution. The apo structure is similar to human TTR with structural changes only at beta-strand D. This strand forms an extended loop conformation similar to the one in chicken TTR. The piscine TTR.T(4) complex shows the T(4)-binding site to be similar but not identical to human TTR, whereas the TTR.T(3) complex shows the I3' halogen situated at the site normally occupied by the hydroxyl group of T(4). The significantly wider entrance of the hormone-binding channel in sea bream TTR, in combination with its narrower cavity, provides a structural explanation for the different binding affinities of human and piscine TTR to T(3) and T(4).


  • Organizational Affiliation
    • Umea Centre for Molecular Pathogenesis, Umea University, SE-901 87 Umea, Sweden.

Macromolecule Content 

  • Total Structure Weight: 56.21 kDa 
  • Atom Count: 3,916 
  • Modeled Residue Count: 463 
  • Deposited Residue Count: 520 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
transthyretin
A, B, C, D
130Sparus aurataMutation(s): 0 
UniProt
Find proteins for Q9PTT3 (Sparus aurata)
Explore Q9PTT3 
Go to UniProtKB:  Q9PTT3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PTT3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.210 (Depositor) 
  • R-Value Work:  0.175 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.497α = 90
b = 58.497β = 90
c = 140.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2014-04-30
    Changes: Data collection
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description