4MYH | pdb_00004myh

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 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

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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 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.

Macromolecule Content 

  • Total Structure Weight: 201.94 kDa 
  • Atom Count: 14,048 
  • Modeled Residue Count: 1,794 
  • Deposited Residue Count: 1,794 
  • Unique protein chains: 1

Macromolecules

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|  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: ATM1, MDY, YMR301C, YM9952.03C
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
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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

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free:  0.290 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
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 


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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