+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31967 | |||||||||
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Title | cryo-EM structure of AMP-PNP bound human ABCB7 | |||||||||
Map data | EM map | |||||||||
Sample |
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Function / homology | Function and homology information ABC-type iron-sulfur cluster transporter activity / positive regulation of iron-sulfur cluster assembly / iron-sulfur cluster export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / iron ion transmembrane transport / heme transmembrane transporter activity / : / Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly ...ABC-type iron-sulfur cluster transporter activity / positive regulation of iron-sulfur cluster assembly / iron-sulfur cluster export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / iron ion transmembrane transport / heme transmembrane transporter activity / : / Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / negative regulation of reactive oxygen species biosynthetic process / transmembrane transport / mitochondrial inner membrane / intracellular iron ion homeostasis / membrane => GO:0016020 / protein homodimerization activity / mitochondrion / ATP binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Yan Q / Yang X / Shen Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: J Struct Biol / Year: 2022 Title: Cryo-EM structure of AMP-PNP-bound human mitochondrial ATP-binding cassette transporter ABCB7. Authors: Qinqin Yan / Yuequan Shen / Xue Yang / Abstract: ATP-binding cassette subfamily B member 7 (ABCB7) is localized in the inner membrane of mitochondria, playing a critical role in iron metabolism. Here, we determined the structure of the ...ATP-binding cassette subfamily B member 7 (ABCB7) is localized in the inner membrane of mitochondria, playing a critical role in iron metabolism. Here, we determined the structure of the nonhydrolyzable ATP analog adenosine-5'-(β-γ-imido) triphosphate (AMP-PNP) bound human ABCB7 at 3.3 Å by single-particle electron cryo-microscopy (cryo-EM). The AMP-PNP-bound human ABCB7 shows an inverted V-shaped homodimeric architecture with an inward-facing open conformation. One AMP-PNP molecule and Mg were identified in each nucleotide-binding domain (NBD) of the hABCB7 monomer. Moreover, four disease-causing missense mutations of human ABCB7 have been mapped to the structure, creating a hotspot map for X-linked sideroblastic anemia and ataxia disease. Our results provide a structural basis for further understanding the transport mechanism of the mitochondrial ABC transporter. | |||||||||
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_31967.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-31967-v30.xml emd-31967.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_31967.png | 42.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31967 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31967 | HTTPS FTP |
-Related structure data
Related structure data | 7vgfMC 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_31967.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 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 ABCB7
Entire | Name: human ABCB7 |
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Components |
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-Supramolecule #1: human ABCB7
Supramolecule | Name: human ABCB7 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Experimental: 150 kDa/nm |
-Macromolecule #1: Iron-sulfur clusters transporter ABCB7, mitochondrial
Macromolecule | Name: Iron-sulfur clusters transporter ABCB7, 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: 76.879914 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGNSGQFLDA AKALQVWPLI EKRTCWHGHA GGGLHTDPKE GLKDVDTRKI IKAMLSYVWP KDRPDLRARV AISLGFLGGA KAMNIVVPF MFKYAVDSLN QMSGNMLNLS DAPNTVATMA TAVLIGYGVS RAGAAFFNEV RNAVFGKVAQ NSIRRIAKNV F LHLHNLDL ...String: MGNSGQFLDA AKALQVWPLI EKRTCWHGHA GGGLHTDPKE GLKDVDTRKI IKAMLSYVWP KDRPDLRARV AISLGFLGGA KAMNIVVPF MFKYAVDSLN QMSGNMLNLS DAPNTVATMA TAVLIGYGVS RAGAAFFNEV RNAVFGKVAQ NSIRRIAKNV F LHLHNLDL GFHLSRQTGA LSKAIDRGTR GISFVLSALV FNLLPIMFEV MLVSGVLYYK CGAQFALVTL GTLGTYTAFT VA VTRWRTR FRIEMNKADN DAGNAAIDSL LNYETVKYFN NERYEAQRYD GFLKTYETAS LKSTSTLAML NFGQSAIFSV GLT AIMVLA SQGIVAGTLT VGDLVMVNGL LFQLSLPLNF LGTVYRETRQ ALIDMNTLFT LLKVDTQIKD KVMASPLQIT PQTA TVAFD NVHFEYIEGQ KVLSGISFEV PAGKKVAIVG GSGSGKSTIV RLLFRFYEPQ KGSIYLAGQN IQDVSLESLR RAVGV VPQD AVLFHNTIYY NLLYGNISAS PEEVYAVAKL AGLHDAILRM PHGYDTQVGE RGLKLSGGEK QRVAIARAIL KDPPVI LYD EATSSLDSIT EETILGAMKD VVKHRTSIFI AHRLSTVVDA DEIIVLDQGK VAERGTHHGL LANPHSIYSE MWHTQSS RV QNHDNPKWEA KKENISKEEE RKKLQEEIVN SVKGCGNCSD YKDDDDKDYK DDDDK |
-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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 14 mg/mL |
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Buffer | pH: 6.5 / Details: 1 mM MgCl2 and 5 mM AMP-PNP |
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 39927 |