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Yorodumi- EMDB-39534: Cryo-EM structure of the human ABCB6 in complex with Cd(II):GSH -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39534 | ||||||||||||
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Title | Cryo-EM structure of the human ABCB6 in complex with Cd(II):GSH | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Cryo-EM / ABC transporter / ATP-binding cassette transporter B6 / ABCB6 / heme biosynthesis / heavy metal detoxification / glutathione / phytochelatin / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information Defective ABCB6 causes MCOPCB7 / cellular detoxification of cadmium ion / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme transport / heme metabolic process / porphyrin-containing compound biosynthetic process ...Defective ABCB6 causes MCOPCB7 / cellular detoxification of cadmium ion / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme transport / heme metabolic process / porphyrin-containing compound biosynthetic process / melanosome assembly / heme transmembrane transport / ABC-type heme transporter activity / melanosome membrane / multivesicular body membrane / endolysosome membrane / mitochondrial envelope / vacuolar membrane / skin development / efflux transmembrane transporter activity / intracellular copper ion homeostasis / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / brain development / transmembrane transport / early endosome membrane / intracellular iron ion homeostasis / mitochondrial outer membrane / endosome / lysosomal membrane / Golgi membrane / heme binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Choi SH / Lee SS / Lee HY / Kim S / Kim JW / Jin MS | ||||||||||||
Funding support | Korea, Republic Of, 3 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Cryo-EM structure of cadmium-bound human ABCB6. Authors: Seung Hun Choi / Sang Soo Lee / Hyeon You Lee / Subin Kim / Ji Won Kim / Mi Sun Jin / Abstract: ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy ...ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy structures of human ABCB6 bound to a cadmium Cd(II) ion in the presence of antioxidant thiol peptides glutathione (GSH) and phytochelatin 2 (PC2) at resolutions of 3.2 and 3.1 Å, respectively. The overall folding of the two structures resembles the inward-facing apo state but with less separation between the two halves of the transporter. Two GSH molecules are symmetrically bound to the Cd(II) ion in a bent conformation, with the central cysteine protruding towards the metal. The N-terminal glutamate and C-terminal glycine of GSH do not directly interact with Cd(II) but contribute to neutralizing positive charges of the binding cavity by forming hydrogen bonds and van der Waals interactions with nearby residues. In the presence of PC2, Cd(II) binding to ABCB6 is similar to that observed with GSH, except that two cysteine residues of each PC2 molecule participate in Cd(II) coordination to form a tetrathiolate. Structural comparison of human ABCB6 and its homologous Atm-type transporters indicate that their distinct substrate specificity might be attributed to variations in the capping residues situated at the top of the substrate-binding cavity. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39534.map.gz | 41.8 MB | EMDB map data format | |
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Header (meta data) | emd-39534-v30.xml emd-39534.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39534_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_39534.png | 75.3 KB | ||
Filedesc metadata | emd-39534.cif.gz | 6 KB | ||
Others | emd_39534_half_map_1.map.gz emd_39534_half_map_2.map.gz | 77.4 MB 77.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39534 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39534 | HTTPS FTP |
-Validation report
Summary document | emd_39534_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_39534_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_39534_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_39534_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39534 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39534 | HTTPS FTP |
-Related structure data
Related structure data | 8yr3MC 8yr4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_39534.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_39534_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39534_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimer complex of ATP-binding cassette transporter B6 in compl...
Entire | Name: Homodimer complex of ATP-binding cassette transporter B6 in complex with Cd(II):GSH |
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Components |
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-Supramolecule #1: Homodimer complex of ATP-binding cassette transporter B6 in compl...
Supramolecule | Name: Homodimer complex of ATP-binding cassette transporter B6 in complex with Cd(II):GSH type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 143.2 kDa/nm |
-Macromolecule #1: ATP-binding cassette sub-family B member 6
Macromolecule | Name: ATP-binding cassette sub-family B member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type heme transporter |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 71.719039 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: APGLRPQSYT LQVHEEDQDV ERSQVRSAAQ QSTWRDFGRK LRLLSGYLWP RGSPALQLVV LICLGLMGLE RALNVLVPIF YRNIVNLLT EKAPWNSLAW TVTSYVFLKF LQGGGTGSTG FVSNLRTFLW IRVQQFTSRR VELLIFSHLH ELSLRWHLGR R TGEVLRIA ...String: APGLRPQSYT LQVHEEDQDV ERSQVRSAAQ QSTWRDFGRK LRLLSGYLWP RGSPALQLVV LICLGLMGLE RALNVLVPIF YRNIVNLLT EKAPWNSLAW TVTSYVFLKF LQGGGTGSTG FVSNLRTFLW IRVQQFTSRR VELLIFSHLH ELSLRWHLGR R TGEVLRIA DRGTSSVTGL LSYLVFNVIP TLADIIIGII YFSMFFNAWF GLIVFLCMSL YLTLTIVVTE WRTKFRRAMN TQ ENATRAR AVDSLLNFET VKYYNAESYE VERYREAIIK YQGLEWKSSA SLVLLNQTQN LVIGLGLLAG SLLCAYFVTE QKL QVGDYV LFGTYIIQLY MPLNWFGTYY RMIQTNFIDM ENMFDLLKEE TEVKDLPGAG PLRFQKGRIE FENVHFSYAD GRET LQDVS FTVMPGQTLA LVGPSGAGKS TILRLLFRFY DISSGCIRID GQDISQVTQA SLRSHIGVVP QDTVLFNDTI ADNIR YGRV TAGNDEVEAA AQAAGIHDAI MAFPEGYRTQ VGERGLKLSG GEKQRVAIAR TILKAPGIIL LDEATSALDT SNERAI QAS LAKVCANRTT IVVAHRLSTV VNADQILVIK DGCIVERGRH EALLSRGGVY ADMWQLQQGQ EETSEDTKPQ TMER UniProtKB: ATP-binding cassette sub-family B member 6 |
-Macromolecule #2: GLUTATHIONE
Macromolecule | Name: GLUTATHIONE / type: ligand / ID: 2 / Number of copies: 2 / Formula: GSH |
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Molecular weight | Theoretical: 307.323 Da |
Chemical component information | ChemComp-GSH: |
-Macromolecule #3: CADMIUM ION
Macromolecule | Name: CADMIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CD |
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Molecular weight | Theoretical: 112.411 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |