5VDE

Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structures of a copper-bound metallochaperone from Saccharomyces cerevisiae.

Lee, M.Cooray, N.D.G.Maher, M.J.

(2017) J. Inorg. Biochem. 177: 368-374

  • DOI: 10.1016/j.jinorgbio.2017.08.009
  • Primary Citation of Related Structures:  5VDF

  • PubMed Abstract: 
  • Atx1 is a metallochaperone protein from the yeast Saccharomyces cerevisiae (yAtx1) that plays a major role in copper homeostasis in this organism. yAtx1 functions as a copper transfer protein by shuttling copper to the secretory pathway to control in ...

    Atx1 is a metallochaperone protein from the yeast Saccharomyces cerevisiae (yAtx1) that plays a major role in copper homeostasis in this organism. yAtx1 functions as a copper transfer protein by shuttling copper to the secretory pathway to control intracellular copper levels. Here we describe the first crystal structures of yAtx1 that have been determined in the presence of Cu(I). The structures from two different crystal forms have been solved and refined to resolutions of 1.65 and 1.93Å. In contrast to the previous metallated crystal structure of yAtx1 where a single Hg(II) atom was coordinated by one yAtx1 molecule, the Cu(I)-yAtx1 was crystallised as a dimer in both crystal forms, sharing one Cu(I) atom between two yAtx1 molecules. This is consistent with the crystal structure of the human homologue Cu(I)-hAtox1. Overall the structures in the two different crystal forms of Cu(I)-yAtx1 are remarkably similar to that of Cu(I)-hAtox1. However, subtle structural differences between Cu(I)-yCtr1 and Cu(I)-hAtox1 are observed in copper coordination geometries and in the conformations of Loop 2, with the latter potentially contributing to differential interactions and copper transfer mechanisms with membrane transport copper uptake systems.


    Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. Electronic address: mihwa.lee@latrobe.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metal homeostasis factor ATX1
A, B, C, D
73Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATX1
Find proteins for P38636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38636
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download SDF File 
Download CCD File 
A, C
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.976α = 90.00
b = 80.054β = 99.91
c = 50.763γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-02 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Lee, M., Maher, M.J.

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release