3OER

Crystal structure of trimeric frataxin from the yeast saccharomyces cerevisiae, complexed with cobalt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering.

Soderberg, C.A.Shkumatov, A.V.Rajan, S.Gakh, O.Svergun, D.I.Isaya, G.Al-Karadaghi, S.

(2011) J.Mol.Biol. 414: 783-797

  • DOI: 10.1016/j.jmb.2011.10.034
  • Primary Citation of Related Structures:  3OEQ
  • Also Cited By: 4EC2

  • PubMed Abstract: 
  • Frataxin is a mitochondrial protein with a central role in iron homeostasis. Defects in frataxin function lead to Friedreich's ataxia, a progressive neurodegenerative disease with childhood onset. The function of frataxin has been shown to be closely ...

    Frataxin is a mitochondrial protein with a central role in iron homeostasis. Defects in frataxin function lead to Friedreich's ataxia, a progressive neurodegenerative disease with childhood onset. The function of frataxin has been shown to be closely associated with its ability to form oligomeric species; however, the factors controlling oligomerization and the types of oligomers present in solution are a matter of debate. Using small-angle X-ray scattering, we found that Co(2+), glycerol, and a single amino acid substitution at the N-terminus, Y73A, facilitate oligomerization of yeast frataxin, resulting in a dynamic equilibrium between monomers, dimers, trimers, hexamers, and higher-order oligomers. Using X-ray crystallography, we found that Co(2+) binds inside the channel at the 3-fold axis of the trimer, which suggests that the metal has an oligomer-stabilizing role. The results reveal the types of oligomers present in solution and support our earlier suggestions that the trimer is the main building block of yeast frataxin oligomers. They also indicate that different mechanisms may control oligomer stability and oligomerization in vivo.


    Related Citations: 
    • The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron
      Karlberg, T.,Schagerlof, U.,Gakh, O.,Park, S.,Ryde, U.,Lindahl, M.,Lleath, K.,Garman, E.,Isaya, G.,Al-Karadaghi, S.
      (2006) Structure 14: 1535


    Organizational Affiliation

    Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, SE-221 00 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Frataxin homolog, mitochondrial
A
123Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YFH1
EC: 1.16.3.1
Find proteins for Q07540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07540
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 121.200α = 90.00
b = 121.200β = 90.00
c = 121.200γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-12-21
    Type: Database references