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Yorodumi- PDB-8khf: Structure of the human ATP synthase bound to bedaquiline (membran... -
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-Basic information
Entry | Database: PDB / ID: 8khf | ||||||||||||
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Title | Structure of the human ATP synthase bound to bedaquiline (membrane domain) | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ATP synthase / Human / cryo-EM | ||||||||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, stator stalk / oxidative phosphorylation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / response to copper ion / mitochondrial proton-transporting ATP synthase complex ...Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, stator stalk / oxidative phosphorylation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / response to copper ion / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / response to hyperoxia / aerobic respiration / substantia nigra development / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / nuclear membrane / mitochondrial inner membrane / hydrolase activity / mitochondrial matrix / lipid binding / mitochondrion / RNA binding / membrane / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | ||||||||||||
Authors | Lai, Y. / Zhang, Y. | ||||||||||||
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 | 8khf.cif.gz | 282.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8khf.ent.gz | 224.4 KB | Display | PDB format |
PDBx/mmJSON format | 8khf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/8khf ftp://data.pdbj.org/pub/pdb/validation_reports/kh/8khf | HTTPS FTP |
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-Related structure data
Related structure data | 37243MC 8j57C 8j58C 8jr0C 8jr1C 8ki3C M: map data used to model this data C: citing same article (ref.) |
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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 F(0) complex subunit ... , 2 types, 9 molecules 12345678K
#1: Protein | Mass: 7610.954 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05496 #5: 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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-ATP synthase subunit ... , 9 types, 9 molecules GHIMNPRST
#2: Protein | Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36542 |
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#3: Protein | Mass: 15029.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30049 |
#4: Protein | Mass: 5790.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56381 |
#6: Protein | Mass: 18383.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75947 |
#7: Protein | Mass: 24833.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00846 |
#8: Protein | Mass: 6673.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56378 |
#10: Protein | Mass: 10804.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56134 |
#11: Protein | Mass: 11309.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75964 |
#12: Protein | Mass: 7947.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56385 |
-Protein / Non-polymers , 2 types, 2 molecules Q
#13: Chemical | ChemComp-BQ1 / |
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#9: Protein | Mass: 8000.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P03928 |
-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-#12 / 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 FIELDBright-field microscopy / 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: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84037 / Symmetry type: POINT |