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 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1016/j.jinorgbio.2017.08.009
  • Primary Citation of Related Structures:  
    5VDE, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metal homeostasis factor ATX1
A, B, C, D
73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ATX1YNL259CN0840
UniProt
Find proteins for P38636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38636 
Go to UniProtKB:  P38636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38636
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.976α = 90
b = 80.054β = 99.91
c = 50.763γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description