+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30609 | ||||||||||||
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Title | Cryo-EM structure of human ABCB6 transporter | ||||||||||||
Map data | map for the full-length ABCB6 | ||||||||||||
Sample |
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Keywords | Transporter / Dimer / Porphyrins / Heme / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / heme transport / tetrapyrrole binding / heme metabolic process / porphyrin-containing compound biosynthetic process ...cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / heme transport / tetrapyrrole binding / heme metabolic process / porphyrin-containing compound biosynthetic process / melanosome assembly / heme transmembrane transport / ABC-type heme transporter activity / melanosome membrane / multivesicular body membrane / mitochondrial envelope / endolysosome membrane / 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 / Resolution: 5.2 Å | ||||||||||||
Authors | Wang C / Cao C | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Protein Sci / Year: 2020 Title: Cryo-electron microscopy structure of human ABCB6 transporter. Authors: Chunyu Wang / Can Cao / Nan Wang / Xiangxi Wang / Xianping Wang / Xuejun C Zhang / Abstract: Human ATP-binding cassette transporter 6 of subfamily B (ABCB6) is an ABC transporter involved in the translocation toxic metals and anti-cancer drugs. Using cryo-electron microscopy, we determined ...Human ATP-binding cassette transporter 6 of subfamily B (ABCB6) is an ABC transporter involved in the translocation toxic metals and anti-cancer drugs. Using cryo-electron microscopy, we determined the molecular structure of full-length ABCB6 in an apo state. The structure of ABCB6 unravels the architecture of a full-length ABCB transporter that harbors two N-terminal transmembrane domains which is indispensable for its ATPase activity in our in vitro assay. A slit-like substrate binding pocket of ABCB6 may accommodate the planar shape of porphyrins, and the existence of a secondary cavity near the mitochondrial intermembrane space side would further facilitate substrate release. Furthermore, the ATPase activity of ABCB6 stimulated with a variety of porphyrin substrates showed different profiles in the presence of glutathione (GSH), suggesting the action of a distinct substrate translocation mechanism depending on the use of GSH as a cofactor. | ||||||||||||
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_30609.map.gz | 62.7 MB | EMDB map data format | |
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Header (meta data) | emd-30609-v30.xml emd-30609.xml | 11 KB 11 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30609_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_30609.png | 11.6 KB | ||
Filedesc metadata | emd-30609.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30609 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30609 | HTTPS FTP |
-Validation report
Summary document | emd_30609_validation.pdf.gz | 543.7 KB | Display | EMDB validaton report |
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Full document | emd_30609_full_validation.pdf.gz | 543.3 KB | Display | |
Data in XML | emd_30609_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_30609_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30609 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30609 | HTTPS FTP |
-Related structure data
Related structure data | 7d7nMC 7d7rC 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_30609.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map for the full-length ABCB6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 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 : Human ABCB6 protein homodimer.
Entire | Name: Human ABCB6 protein homodimer. |
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Components |
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-Supramolecule #1: Human ABCB6 protein homodimer.
Supramolecule | Name: Human ABCB6 protein homodimer. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: ATP-binding cassette sub-family B member 6, mitochondrial
Macromolecule | Name: ATP-binding cassette sub-family B member 6, mitochondrial type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 93.974172 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVTVGNYCEA EGPVGPAWMQ DGLSPCFFFT LVPSTRMALG TLALVLALPC RRRERPAGAD SLSWGAGPRI SPYVLQLLLA TLQAALPLA GLAGRVGTAR GAPLPSYLLL ASVLESLAGA CGLWLLVVER SQARQRLAMG IWIKFRHSPG LLLLWTVAFA A ENLALVSW ...String: MVTVGNYCEA EGPVGPAWMQ DGLSPCFFFT LVPSTRMALG TLALVLALPC RRRERPAGAD SLSWGAGPRI SPYVLQLLLA TLQAALPLA GLAGRVGTAR GAPLPSYLLL ASVLESLAGA CGLWLLVVER SQARQRLAMG IWIKFRHSPG LLLLWTVAFA A ENLALVSW NSPQWWWARA DLGQQVQFSL WVLRYVVSGG LFVLGLWAPG LRPQSYTLQV HEEDQDVERS QVRSAAQQST WR DFGRKLR LLSGYLWPRG SPALQLVVLI CLGLMGLERA LNVLVPIFYR NIVNLLTEKA PWNSLAWTVT SYVFLKFLQG GGT GSTGFV SNLRTFLWIR VQQFTSRRVE LLIFSHLHEL SLRWHLGRRT GEVLRIADRG TSSVTGLLSY LVFNVIPTLA DIII GIIYF SMFFNAWFGL IVFLCMSLYL TLTIVVTEWR TKFRRAMNTQ ENATRARAVD SLLNFETVKY YNAESYEVER YREAI IKYQ GLEWKSSASL VLLNQTQNLV IGLGLLAGSL LCAYFVTEQK LQVGDYVLFG TYIIQLYMPL NWFGTYYRMI QTNFID MEN MFDLLKEETE VKDLPGAGPL RFQKGRIEFE NVHFSYADGR ETLQDVSFTV MPGQTLALVG PSGAGKSTIL RLLFRFY DI SSGCIRIDGQ DISQVTQASL RSHIGVVPQD TVLFNDTIAD NIRYGRVTAG NDEVEAAAQA AGIHDAIMAF PEGYRTQV G ERGLKLSGGE KQRVAIARTI LKAPGIILLD EATSALDTSN ERAIQASLAK VCANRTTIVV AHRLSTVVNA DQILVIKDG CIVERGRHEA LLSRGGVYAD MWQLQQGQEE TSEDTKPQTM ER UniProtKB: ATP-binding cassette sub-family B member 6 |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 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 |