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Yorodumi- PDB-8j0t: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in t... -
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-Basic information
Entry | Database: PDB / ID: 8j0t | ||||||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in the apo-form | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ATP synthase / Mycobacterium tuberculosis / cryo-EM | ||||||||||||
Function / homology | Function and homology information photosynthetic electron transport in photosystem I / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall ...photosynthetic electron transport in photosystem I / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Zhang, Y. / Lai, Y. / Liu, F. / Rao, Z. / 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 | 8j0t.cif.gz | 805.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j0t.ent.gz | 666.3 KB | Display | PDB format |
PDBx/mmJSON format | 8j0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/8j0t ftp://data.pdbj.org/pub/pdb/validation_reports/j0/8j0t | HTTPS FTP |
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-Related structure data
Related structure data | 35911MC 8j0sC 8j57C 8j58C 8jr0C 8jr1C 8khfC 8ki3C 37029 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 ... , 7 types, 19 molecules ABCDEFGH123456789ab
#1: Protein | Mass: 59358.070 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpA, Rv1308, MTCY373.28 / Production host: Mycolicibacterium smegmatis (bacteria) References: UniProt: P9WPU7, H+-transporting two-sector ATPase #2: Protein | Mass: 53150.934 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpD, Rv1310, MTCY373.30 / Production host: Mycolicibacterium smegmatis (bacteria) References: UniProt: P9WPU5, H+-transporting two-sector ATPase #3: Protein | | Mass: 33929.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpG, Rv1309, MTCY373.29 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: P9WPU9 #4: Protein | | Mass: 13149.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpC, Rv1311, MTCY373.31 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: P9WPV1 #5: Protein | Mass: 8058.423 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpE / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045H4W8 #6: Protein | | Mass: 27488.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: atpB, ERS007657_00358, ERS007661_00092, ERS007663_00105, ERS007665_00910, ERS007670_00031, ERS007679_03316, ERS007681_03471, ERS007688_02939, ERS007703_00159, ERS007720_03212, ERS007722_00190, ...Gene: atpB, ERS007657_00358, ERS007661_00092, ERS007663_00105, ERS007665_00910, ERS007670_00031, ERS007679_03316, ERS007681_03471, ERS007688_02939, ERS007703_00159, ERS007720_03212, ERS007722_00190, ERS007739_02359, ERS007741_03568, ERS024276_02583, ERS027646_02991, ERS027659_00329, ERS027661_00021, SAMEA2683035_01568 Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045J1C5 #7: Protein | | Mass: 18345.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpF / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045H294 |
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-Protein , 1 types, 1 molecules d
#8: Protein | Mass: 48866.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpH / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045JVE3 |
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-Non-polymers , 3 types, 10 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | |
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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: Mycobacterium tuberculosis ATP synthase / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Source (recombinant) | Organism: Mycolicibacterium smegmatis (bacteria) |
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
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66593 / Symmetry type: POINT | ||||||||||||||||||||||||
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