S. cerevisiae Atm1 in MSP1D1 nanodiscs with bound AMP-PNP and Mg2+

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Conformational changes in the yeast mitochondrial ABC transporter Atm1 during the transport cycle.

Ellinghaus, T.L.Marcellino, T.Srinivasan, V.Lill, R.Kuhlbrandt, W.

(2021) Sci Adv 7: eabk2392-eabk2392

  • DOI: https://doi.org/10.1126/sciadv.abk2392
  • Primary Citation of Related Structures:  
    7PSL, 7PSM, 7PSN

  • PubMed Abstract: 

    The mitochondrial inner membrane ABC transporter Atm1 exports an unknown substrate to the cytosol for iron-sulfur protein biogenesis, cellular iron regulation, and tRNA thio-modification. Mutations in the human relative ABCB7 cause the iron storage disease XLSA/A. We determined 3D structures of two complementary states of Atm1 in lipid nanodiscs by electron cryo-microscopy at 2.9- to 3.4-Å resolution. The inward-open structure resembled the known crystal structure of nucleotide-free apo-Atm1 closely. The occluded conformation with bound AMP-PNP-Mg 2+ showed a tight association of the two nucleotide-binding domains, a rearrangement of the C-terminal helices, and closure of the putative substrate-binding cavity in the homodimeric transporter. We identified a hydrophobic patch on the C-terminal helices of yeast Atm1, which is unique among type IV ABC transporters of known structure. Truncation mutants of yeast Atm1 suggest that the C-terminal helices stabilize the dimer, yet are not necessary for closure of the nucleotide-binding domains.

  • Organizational Affiliation

    Max-Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur clusters transporter ATM1, mitochondrial
A, B
607Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ATM1MDYYMR301CYM9952.03C
EC: 7
Membrane Entity: Yes 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyLI 415/5 & SR 113/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release