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- EMDB-13615: S. cerevisiae Atm1 in MSP1E3D1 nanodiscs with bound AMP-PNP and Mg2+ -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13615 | |||||||||
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Title | S. cerevisiae Atm1 in MSP1E3D1 nanodiscs with bound AMP-PNP and Mg2+ | |||||||||
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Function / homology | ![]() iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ellinghaus TL / Kuehlbrandt W | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.7 KB 11.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.8 KB | Display | ![]() |
Images | ![]() | 211.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7psnMC ![]() 7pslC ![]() 7psmC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Atm1 homodimer in MSP1E3D1 nanodiscs
Entire | Name: Atm1 homodimer in MSP1E3D1 nanodiscs |
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Components |
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-Supramolecule #1: Atm1 homodimer in MSP1E3D1 nanodiscs
Supramolecule | Name: Atm1 homodimer in MSP1E3D1 nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 68.392969 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 |
-Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ![]() ChemComp-ANP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: (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: 4 / Number of copies: 4 / Formula: LOP |
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Molecular weight | Theoretical: 661.89 Da |
Chemical component information | ![]() ChemComp-LOP: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 68.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |