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Yorodumi- EMDB-33604: Cryo-EM Structure of apo mitochondrial ABC transporter ABCB10 fro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33604 | |||||||||
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Title | Cryo-EM Structure of apo mitochondrial ABC transporter ABCB10 from Biortus | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | ABCB10 / ABC transporter / biliverdin / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane ...positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 Å | |||||||||
Authors | Cao S / Yang Y | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structures of mitochondrial ABC transporter ABCB10 in apo and biliverdin-bound form. Authors: Sheng Cao / Yihu Yang / Lili He / Yumo Hang / Xiaodong Yan / Hui Shi / Jiaquan Wu / Zhuqing Ouyang / Abstract: ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron ...ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron transporter mitoferrin-1. Recently, it was found that ABCB10 is a mitochondrial biliverdin exporter. However, the molecular mechanism of biliverdin export by ABCB10 remains elusive. Here we report the cryo-EM structures of ABCB10 in apo (ABCB10-apo) and biliverdin-bound form (ABCB10-BV) at 3.67 Å and 2.85 Å resolution, respectively. ABCB10-apo adopts a wide-open conformation and may thus represent the apo form structure. ABCB10-BV forms a closed conformation and biliverdin situates in a hydrophobic pocket in one protomer and bridges the interaction through hydrogen bonds with the opposing one. We also identify cholesterols sandwiched by BVs and discuss the export dynamics based on these structural and biochemical observations. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33604.map.gz | 183.5 MB | EMDB map data format | |
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Header (meta data) | emd-33604-v30.xml emd-33604.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33604_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_33604.png | 27.9 KB | ||
Masks | emd_33604_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-33604.cif.gz | 5.7 KB | ||
Others | emd_33604_additional_1.map.gz emd_33604_half_map_1.map.gz emd_33604_half_map_2.map.gz | 105.9 MB 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33604 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33604 | HTTPS FTP |
-Validation report
Summary document | emd_33604_validation.pdf.gz | 845.8 KB | Display | EMDB validaton report |
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Full document | emd_33604_full_validation.pdf.gz | 845.4 KB | Display | |
Data in XML | emd_33604_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_33604_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33604 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33604 | HTTPS FTP |
-Related structure data
Related structure data | 7y49MC 7y48C 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_33604.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33604_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: original map
File | emd_33604_additional_1.map | ||||||||||||
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Annotation | original map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33604_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33604_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimer of ABCB10, apo form
Entire | Name: Homodimer of ABCB10, apo form |
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Components |
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-Supramolecule #1: Homodimer of ABCB10, apo form
Supramolecule | Name: Homodimer of ABCB10, apo form / 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 10, mitochondrial
Macromolecule | Name: ATP-binding cassette sub-family B member 10, mitochondrial type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 67.180125 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAGLPEARKL LGLAYPERRR LAAAVGFLTM SSVISMSAPF FLGKIIDVIY TNPTVDYSDN LTRLCLGLSA VFLCGAAANA IRVYLMQTS GQRIVNRLRT SLFSSILRQE VAFFDKTRTG ELINRLSSDT ALLGRSVTEN LSDGLRAGAQ ASVGISMMFF V SPNLATFV ...String: MAGLPEARKL LGLAYPERRR LAAAVGFLTM SSVISMSAPF FLGKIIDVIY TNPTVDYSDN LTRLCLGLSA VFLCGAAANA IRVYLMQTS GQRIVNRLRT SLFSSILRQE VAFFDKTRTG ELINRLSSDT ALLGRSVTEN LSDGLRAGAQ ASVGISMMFF V SPNLATFV LSVVPPVSII AVIYGRYLRK LTKVTQDSLA QATQLAEERI GNVRTVRAFG KEMTEIEKYA SKVDHVMQLA RK EAFARAG FFGATGLSGN LIVLSVLYKG GLLMGSAHMT VGELSSFLMY AFWVGISIGG LSSFYSELMK GLGAGGRLWE LLE REPKLP FNEGVILNEK SFQGALEFKN VHFAYPARPE VPIFQDFSLS IPSGSVTALV GPSGSGKSTV LSLLLRLYDP ASGT ISLDG HDIRQLNPVW LRSKIGTVSQ EPILFSCSIA ENIAYGADDP SSVTAEEIQR VAEVANAVAF IRNFPQGFNT VVGEK GVLL SGGQKQRIAI ARALLKNPKI LLLDQATSAL DAENEYLVQE ALDRLMDGRT VLVIAHRLST IKNANMVAVL DQGKIT EYG KHEELLSKPN GIYRKLMNKQ SFISAENLYF QGDYKDDDDK HHHHHHHHHH UniProtKB: ATP-binding cassette sub-family B member 10, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.78 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 10 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.5 sec. / Average electron dose: 55.21 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |