4MYH

Structure of the Glutathione bound mitochondrial ABC transporter, Atm1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of nucleotide-free and glutathione-bound mitochondrial ABC transporter Atm1.

Srinivasan, V.Pierik, A.J.Lill, R.

(2014) Science 343: 1137-1140

  • DOI: https://doi.org/10.1126/science.1246729
  • Primary Citation of Related Structures:  
    4MYC, 4MYH

  • PubMed Abstract: 

    The yeast mitochondrial ABC transporter Atm1, in concert with glutathione, functions in the export of a substrate required for cytosolic-nuclear iron-sulfur protein biogenesis and cellular iron regulation. Defects in the human ortholog ABCB7 cause the sideroblastic anemia XLSA/A. Here, we report the crystal structures of free and glutathione-bound Atm1 in inward-facing, open conformations at 3.06- and 3.38-angstrom resolution, respectively. The glutathione binding site includes a residue mutated in XLSA/A and is located close to the inner membrane surface in a large cavity. The two nucleotide-free adenosine 5'-triphosphate binding domains do not interact yet are kept in close vicinity through tight interaction of the two C-terminal α-helices of the Atm1 dimer. The resulting protein stabilization may be a common structural feature of all ABC exporters.


  • Organizational Affiliation

    Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur clusters transporter ATM1, mitochondrialA,
B [auth C],
C [auth B]
598Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ATM1MDYYMR301CYM9952.03C
EC: 3.6.3.44 (PDB Primary Data), 7 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P40416 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40416 
Go to UniProtKB:  P40416
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40416
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download Ideal Coordinates CCD File 
D [auth B]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.686α = 90
b = 157.686β = 90
c = 523.29γ = 120
Software Package:
Software NamePurpose
SHELXCDphasing
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations