4PVN

Neutron structure of human transthyretin (TTR) at room temperature to 2.3A resolution (monochromatic)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein

Haupt, M.Blakeley, M.P.Fisher, S.J.Mason, S.A.Cooper, J.B.Mitchell, E.P.Forsyth, V.T.

(2014) IUCrJ 1: 429-438

  • DOI: 10.1107/S2052252514021113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit ...

    Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.


    Organizational Affiliation

    Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University , Staffordshire ST5 5BG, United Kingdom ; Institut Laue-Langevin , 71, avenue des Martyrs, Grenoble, CS 20156, France ; Partnership for Structural Biology , 71, avenue des Martyrs, Grenoble, CS 20156, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
130Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOD
Query on DOD

Download SDF File 
Download CCD File 
A, B
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.680α = 90.00
b = 86.260β = 90.00
c = 65.720γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
Software Package:
Software NamePurpose
SCALAdata scaling
MADSYSphasing
PHENIXrefinement
PHENIXphasing
PHENIXmodel building
RETREATdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description