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Yorodumi- PDB-8ki3: Structure of the human ATP synthase bound to bedaquiline (composite) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ki3 | ||||||||||||
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Title | Structure of the human ATP synthase bound to bedaquiline (composite) | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ATP synthase / Human / cryo-EM | ||||||||||||
Function / homology | Function and homology information mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / positive regulation of proteolysis involved in protein catabolic process / Cristae formation / 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 / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / positive regulation of proteolysis involved in protein catabolic process / Cristae formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding / mitochondrial depolarization / ATPase inhibitor activity / 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 / proton-transporting ATP synthase complex / oxidative phosphorylation / cellular response to interleukin-7 / enzyme inhibitor activity / response to copper ion / response to muscle activity / heme biosynthetic process / : / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / : / MHC class I protein binding / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / response to hyperoxia / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton transmembrane transport / Mitochondrial protein degradation / substantia nigra development / aerobic respiration / proton-transporting ATPase activity, rotational mechanism / reactive oxygen species metabolic process / proton-transporting ATP synthase activity, rotational mechanism / cellular response to dexamethasone stimulus / erythrocyte differentiation / generation of precursor metabolites and energy / mitochondrial membrane / regulation of intracellular pH / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / ADP binding / osteoblast differentiation / ATPase binding / nuclear membrane / angiogenesis / response to ethanol / protease binding / mitochondrial inner membrane / 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 / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||||||||
Authors | Lai, Y. / Zhang, Y. / Gong, H. | ||||||||||||
Funding support | China, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ki3.cif.gz | 845.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ki3.ent.gz | 696.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ki3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ki3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8ki3_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ki3_validation.xml.gz | 126.1 KB | Display | |
Data in CIF | 8ki3_validation.cif.gz | 194.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/8ki3 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/8ki3 | HTTPS FTP |
-Related structure data
Related structure data | 37251MC 8j0sC 8j0tC 8j57C 8j58C 8jr0C 8jr1C 8khfC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase subunit ... , 12 types, 16 molecules ABCDEFGOHIMNPRST
#1: Protein | Mass: 55276.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25705 #2: Protein | Mass: 51821.965 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P06576 #3: Protein | | Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36542 #5: Protein | | Mass: 20904.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48047 #7: Protein | | Mass: 15029.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30049 #8: Protein | | Mass: 5790.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56381 #10: Protein | | Mass: 18383.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75947 #11: Protein | | Mass: 24833.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00846 #12: Protein | | Mass: 6673.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56378 #14: Protein | | Mass: 10804.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56134 #15: Protein | | Mass: 11309.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75964 #16: Protein | | Mass: 7947.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56385 |
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-Protein , 3 types, 3 molecules JQL
#4: Protein | Mass: 9540.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UII2 |
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#13: Protein | Mass: 8000.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P03928 |
#17: Protein | Mass: 12606.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18859 |
-ATP synthase F(0) complex subunit ... , 2 types, 9 molecules 12345678K
#6: Protein | Mass: 7610.954 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05496 #9: Protein | | Mass: 24658.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24539 |
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-Non-polymers , 4 types, 11 molecules
#18: Chemical | #19: Chemical | ChemComp-MG / #20: Chemical | #21: Chemical | ChemComp-BQ1 / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human ATP synthase / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84037 / Symmetry type: POINT | ||||||||||||||||||||||||
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