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Yorodumi- EMDB-37251: Structure of the human ATP synthase bound to bedaquiline (composite) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37251 | ||||||||||||
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Title | Structure of the human ATP synthase bound to bedaquiline (composite) | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | ATP synthase / Human / cryo-EM / Membrane protein | ||||||||||||
Function / homology | Function and homology information mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / regulation of protein targeting to mitochondrion / Formation of ATP by chemiosmotic coupling / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / regulation of protein targeting to mitochondrion / Formation of ATP by chemiosmotic coupling / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding / ATPase inhibitor activity / mitochondrial depolarization / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Mitochondrial protein import / negative regulation of ATP-dependent activity / mitochondrial proton-transporting ATP synthase complex assembly / negative regulation of hydrolase activity / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / enzyme inhibitor activity / proton-transporting ATP synthase complex / cellular response to interleukin-7 / oxidative phosphorylation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / response to muscle activity / response to copper ion / heme biosynthetic process / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / negative regulation of endothelial cell proliferation / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / cellular response to nitric oxide / response to hyperoxia / proton-transporting ATP synthase complex, catalytic core F(1) / positive regulation of blood vessel endothelial cell migration / MHC class I protein binding / aerobic respiration / H+-transporting two-sector ATPase / substantia nigra development / proton-transporting ATPase activity, rotational mechanism / reactive oxygen species metabolic process / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cellular response to dexamethasone stimulus / erythrocyte differentiation / generation of precursor metabolites and energy / ADP binding / regulation of intracellular pH / mitochondrial membrane / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / osteoblast differentiation / ATPase binding / angiogenesis / response to ethanol / nuclear membrane / mitochondrial inner membrane / protease binding / calmodulin binding / hydrolase activity / mitochondrial matrix / membrane raft / lipid binding / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||||||||
Authors | Lai Y / Zhang Y / Gong H | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: Structure of Mycobacterium tuberculosis ATP synthase Authors: Zhang Y / Lai Y / Liu F / Rao Z / Gong H | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37251.map.gz | 468.4 MB | EMDB map data format | |
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Header (meta data) | emd-37251-v30.xml emd-37251.xml | 27.1 KB 27.1 KB | Display Display | EMDB header |
Images | emd_37251.png | 41.8 KB | ||
Filedesc metadata | emd-37251.cif.gz | 7.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37251 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37251 | HTTPS FTP |
-Related structure data
Related structure data | 8ki3MC 8j57C 8j58C 8jr0C 8jr1C 8khfC C: citing same article (ref.) M: atomic model generated by this map |
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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_37251.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.73 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : human ATP synthase
+Supramolecule #1: human ATP synthase
+Macromolecule #1: ATP synthase subunit alpha, mitochondrial
+Macromolecule #2: ATP synthase subunit beta, mitochondrial
+Macromolecule #3: ATP synthase subunit gamma, mitochondrial
+Macromolecule #4: ATPase inhibitor, mitochondrial
+Macromolecule #5: ATP synthase subunit O, mitochondrial
+Macromolecule #6: ATP synthase F(0) complex subunit C1, mitochondrial
+Macromolecule #7: ATP synthase subunit delta, mitochondrial
+Macromolecule #8: ATP synthase subunit epsilon, mitochondrial
+Macromolecule #9: ATP synthase F(0) complex subunit B1, mitochondrial
+Macromolecule #10: ATP synthase subunit d, mitochondrial
+Macromolecule #11: ATP synthase subunit a
+Macromolecule #12: ATP synthase subunit ATP5MJ, mitochondrial
+Macromolecule #13: ATP synthase protein 8
+Macromolecule #14: ATP synthase subunit f, mitochondrial
+Macromolecule #15: ATP synthase subunit g, mitochondrial
+Macromolecule #16: ATP synthase subunit e, mitochondrial
+Macromolecule #17: ATP synthase-coupling factor 6, mitochondrial
+Macromolecule #18: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #21: Bedaquiline
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84037 |