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Structure paper

TitleConformational changes in the yeast mitochondrial ABC transporter Atm1 during the transport cycle.
Journal, issue, pagesSci Adv, Vol. 7, Issue 52, Page eabk2392, Year 2021
Publish dateDec 24, 2021
AuthorsThomas L Ellinghaus / Thomas Marcellino / Vasundara Srinivasan / Roland Lill / Werner Kühlbrandt /
PubMed AbstractThe 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 ...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 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.
External linksSci Adv / PubMed:34936443 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 7.1 Å
Structure data

13613

7psl

EMDB-13613, PDB-7psl:
S. cerevisiae Atm1 in MSP1D1 nanodiscs in nucleotide-free state
Method: EM (single particle) / Resolution: 3.3 Å

13614

7psm

EMDB-13614, PDB-7psm:
S. cerevisiae Atm1 in MSP1D1 nanodiscs with bound AMP-PNP and Mg2+
Method: EM (single particle) / Resolution: 3.4 Å

13615

7psn

EMDB-13615, PDB-7psn:
S. cerevisiae Atm1 in MSP1E3D1 nanodiscs with bound AMP-PNP and Mg2+
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-13616:
C. thermophilum Atm1 in MSP1E3D1 nanodiscs in nucleotide-free state, class 1
Method: EM (single particle) / Resolution: 7.1 Å

EMDB-13617:
C. thermophilum Atm1 in MSP1E3D1 nanodiscs in nucleotide-free state, class 2
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-13618:
C. thermophilum Atm1 in MSP1E3D1 nanodiscs in nucleotide-free state, class 3
Method: EM (single particle) / Resolution: 4.2 Å

Chemicals

ChemComp-LOP:
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / phospholipid*YM

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • Saccharomyces cerevisiae (brewer's yeast)
  • Chaetomium thermophilum (fungus)
KeywordsTRANSPORT PROTEIN / ABC transporter

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