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Yorodumi- PDB-8jr0: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in c... -
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-Basic information
Entry | Database: PDB / ID: 8jr0 | ||||||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587 | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ATP synthase / Mycobacterium tuberculosis / cryo-EM | ||||||||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem I / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / photosynthetic electron transport in photosystem II / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem I / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / photosynthetic electron transport in photosystem II / 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 | 8jr0.cif.gz | 810.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jr0.ent.gz | 672.2 KB | Display | PDB format |
PDBx/mmJSON format | 8jr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jr0_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8jr0_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8jr0_validation.xml.gz | 115.7 KB | Display | |
Data in CIF | 8jr0_validation.cif.gz | 180.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/8jr0 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/8jr0 | HTTPS FTP |
-Related structure data
Related structure data | 36589MC 8j0sC 8j0tC 8j57C 8j58C 8jr1C 8khfC 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 ... , 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 , 4 types, 17 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | #12: Chemical | ChemComp-UTI / ( Mass: 614.503 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C30H33BrFN3O5 |
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-Details
Has ligand of interest | N |
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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-#4 / 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 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81528 / Symmetry type: POINT | ||||||||||||||||||||||||
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