+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13606 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of CtAtm1 in the inward-facing open conformation | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Keywords | ABC exporter / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information ABC-type transporter activity / intracellular iron ion homeostasis / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Thermochaetoides thermophila DSM 1495 (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||||||||
Authors | Li P / Wang KT / Gourdon PE | ||||||||||||
Funding support | Denmark, 3 items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria. Authors: Ping Li / Amber L Hendricks / Yong Wang / Rhiza Lyne E Villones / Karin Lindkvist-Petersson / Gabriele Meloni / J A Cowan / Kaituo Wang / Pontus Gourdon / Abstract: In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest ...In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest mitochondrial ABCB7-type exporters are involved in maturation of cytosolic iron-sulfur proteins. However, the molecular mechanism for how the ABCB7-type exporters participate in this process remains elusive. Here, we report a series of cryo-electron microscopy structures of a eukaryotic homolog of human ABCB7, CtAtm1, determined at average resolutions ranging from 2.8 to 3.2 Å, complemented by functional characterization and molecular docking in silico. We propose that CtAtm1 accepts delivery from glutathione-complexed iron-sulfur clusters. A partially occluded state links cargo-binding to residues at the mitochondrial matrix interface that line a positively charged cavity, while the binding region becomes internalized and is partially divided in an early occluded state. Collectively, our findings substantially increase the understanding of the transport mechanism of eukaryotic ABCB7-type proteins. | ||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_13606.map.gz | 64.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-13606-v30.xml emd-13606.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13606_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_13606.png | 48 KB | ||
Filedesc metadata | emd-13606.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13606 | HTTPS FTP |
-Validation report
Summary document | emd_13606_validation.pdf.gz | 516.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_13606_full_validation.pdf.gz | 516.1 KB | Display | |
Data in XML | emd_13606_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_13606_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13606 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13606 | HTTPS FTP |
-Related structure data
Related structure data | 7pqxMC 7pr1C 7proC 7pruC 7psdC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_13606.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : atm1 dimer
Entire | Name: atm1 dimer |
---|---|
Components |
|
-Supramolecule #1: atm1 dimer
Supramolecule | Name: atm1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
-Macromolecule #1: Putative iron-sulfur protein
Macromolecule | Name: Putative iron-sulfur protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 77.200805 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSPRSRLLAS SLRGGLLLRP CSARRSTLLN PSPSPLRKAI FHTTSLRAFK NLAEIATSSK EDASSLKPKG KPSPPGDPLA TIEKTAAEQ RRADWAIIKQ MSRYLWPKDS WSDKARVLLA LSLLVGGKVL NVHVPFYFRE IIDRLNIDVA AVGGTVSAVA G AVIFAYGA ...String: MSPRSRLLAS SLRGGLLLRP CSARRSTLLN PSPSPLRKAI FHTTSLRAFK NLAEIATSSK EDASSLKPKG KPSPPGDPLA TIEKTAAEQ RRADWAIIKQ MSRYLWPKDS WSDKARVLLA LSLLVGGKVL NVHVPFYFRE IIDRLNIDVA AVGGTVSAVA G AVIFAYGA SRIGAVVSQE LRNAVFSSVA QKAIRRVATQ TFGHLLNLDL SFHLSKQTGG LTRAIDRGTK GISYLLTSMV FH IVPTALE IGMVCGILTY QFGWEFAAIT AATMAAYTAF TITTTAWRTK FRRQANAADN AASTVAVDSL INYEAVKYFN NEA YEIARY DKALQAYERS SIKVATSLAF LNSGQNIIFS SALTLMMWLG ARGVLAGDLS VGDLVLINQL VFQLSVPLNF LGSV YRELR QSLLDMETLF DLQKVNVTIR EAPNAKPLAL PKGGEIRFEN VTFGYYPDRP ILRNLSLTIP AGKKVAVVGP SGCGK STLL RLLFRSYDPQ QGKIFIDDQD IKSVTLESLR KSIGVVPQDT PLFNDTVELN IRYGNVNATQ EQVIAAAQKA HIHEKI ISW PHGYQTRVGE RGLMISGGEK QRLAVSRLIL KDPPLLFFDE ATSALDTHTE QALMANINEV VKEKKRTALF VAHRLRT IY DADLIIVLKE GVVVEQGSHR ELMERDGVYA ELWMAQEMLH QGEAAEEPAE GEKAEEKK UniProtKB: Iron-sulfur clusters transporter ATM1, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |