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Yorodumi- EMDB-13613: S. cerevisiae Atm1 in MSP1D1 nanodiscs in nucleotide-free state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13613 | |||||||||
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Title | S. cerevisiae Atm1 in MSP1D1 nanodiscs in nucleotide-free state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / intracellular iron ion homeostasis ...iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / intracellular iron ion homeostasis / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Ellinghaus TL / Kuehlbrandt W | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Conformational changes in the yeast mitochondrial ABC transporter Atm1 during the transport cycle. Authors: Thomas L Ellinghaus / Thomas Marcellino / Vasundara Srinivasan / Roland Lill / Werner Kühlbrandt / 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 ...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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13613.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-13613-v30.xml emd-13613.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13613_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_13613.png | 240 KB | ||
Filedesc metadata | emd-13613.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13613 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13613 | HTTPS FTP |
-Validation report
Summary document | emd_13613_validation.pdf.gz | 498.7 KB | Display | EMDB validaton report |
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Full document | emd_13613_full_validation.pdf.gz | 498.3 KB | Display | |
Data in XML | emd_13613_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_13613_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13613 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13613 | HTTPS FTP |
-Related structure data
Related structure data | 7pslMC 7psmC 7psnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13613.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Atm1 homodimer in MSP1D1 nanodiscs
Entire | Name: Atm1 homodimer in MSP1D1 nanodiscs |
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Components |
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-Supramolecule #1: Atm1 homodimer in MSP1D1 nanodiscs
Supramolecule | Name: Atm1 homodimer in MSP1D1 nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Molecular weight | Theoretical: 137 KDa |
-Macromolecule #1: Iron-sulfur clusters transporter ATM1, mitochondrial
Macromolecule | Name: Iron-sulfur clusters transporter ATM1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Translocases |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 68.392969 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: LKDLFRYIWP KGNNKVRIRV LIALGLLISA KILNVQVPFF FKQTIDSMNI AWDDPTVALP AAIGLTILCY GVARFGSVLF GELRNAVFA KVAQNAIRTV SLQTFQHLMK LDLGWHLSRQ TGGLTRAMDR GTKGISQVLT AMVFHIIPIS FEISVVCGIL T YQFGASFA ...String: LKDLFRYIWP KGNNKVRIRV LIALGLLISA KILNVQVPFF FKQTIDSMNI AWDDPTVALP AAIGLTILCY GVARFGSVLF GELRNAVFA KVAQNAIRTV SLQTFQHLMK LDLGWHLSRQ TGGLTRAMDR GTKGISQVLT AMVFHIIPIS FEISVVCGIL T YQFGASFA AITFSTMLLY SIFTIKTTAW RTHFRRDANK ADNKAASVAL DSLINFEAVK YFNNEKYLAD KYNGSLMNYR DS QIKVSQS LAFLNSGQNL IFTTALTAMM YMGCTGVIGG NLTVGDLVLI NQLVFQLSVP LNFLGSVYRD LKQSLIDMET LFK LRKNEV KIKNAERPLM LPENVPYDIT FENVTFGYHP DRKILKNASF TIPAGWKTAI VGSSGSGKST ILKLVFRFYD PESG RILIN GRDIKEYDID ALRKVIGVVP QDTPLFNDTI WENVKFGRID ATDEEVITVV EKAQLAPLIK KLPQGFDTIV GERGL MISG GEKQRLAIAR VLLKNARIMF FDEATSALDT HTEQALLRTI RDNFTSGSRT SVYIAHRLRT IADADKIIVL DNGRVR EEG KHLELLAMPG SLYRELWTIQ EDLDHLENEL KDQQELWSHP QFEK UniProtKB: Iron-sulfur clusters transporter ATM1, mitochondrial |
-Macromolecule #2: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANO...
Macromolecule | Name: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE type: ligand / ID: 2 / Number of copies: 2 / Formula: LOP |
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Molecular weight | Theoretical: 661.89 Da |
Chemical component information | ChemComp-LOP: |
-Macromolecule #3: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |