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Yorodumi- PDB-5tj5: Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tj5 | |||||||||||||||
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Title | Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase | |||||||||||||||
Components | (V-type proton ATPase subunit ...) x 7 | |||||||||||||||
Keywords | MOTOR PROTEIN / Rotary ATPase / Vacuolar-type ATPase / Electron Cryomicroscopy / Vo region / Membrane protein | |||||||||||||||
Function / homology | Function and homology information protein localization to vacuolar membrane / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...protein localization to vacuolar membrane / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / protein targeting to vacuole / vacuole organization / cellular hyperosmotic response / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / phosphatidylinositol-3,5-bisphosphate binding / fungal-type vacuole membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / membrane Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||
Authors | Mazhab-Jafari, M.T. / Rohou, A. / Schmidt, C. / Bueler, S.A. / Benlekbir, S. / Robinson, C.V. / Rubinstein, J.L. | |||||||||||||||
Funding support | Canada, United Kingdom, European Union, 4items
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Citation | Journal: Nature / Year: 2016 Title: Atomic model for the membrane-embedded V motor of a eukaryotic V-ATPase. Authors: Mohammad T Mazhab-Jafari / Alexis Rohou / Carla Schmidt / Stephanie A Bueler / Samir Benlekbir / Carol V Robinson / John L Rubinstein / Abstract: Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney ...Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V region drives proton translocation through the membrane-embedded V region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V and V regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits acc'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5tj5.cif.gz | 358.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tj5.ent.gz | 265.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tj5_validation.pdf.gz | 966 KB | Display | wwPDB validaton report |
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Full document | 5tj5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5tj5_validation.xml.gz | 63.4 KB | Display | |
Data in CIF | 5tj5_validation.cif.gz | 99.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tj5 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tj5 | HTTPS FTP |
-Related structure data
Related structure data | 8409MC 8363C 8364C 8367C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-V-type proton ATPase subunit ... , 7 types, 14 molecules ABDEFGHIJMNLOP
#1: Protein | Mass: 70067.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32563 | ||||||
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#2: Protein | Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P23968 | ||||||
#3: Protein | Mass: 15195.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32842 | ||||||
#4: Protein | Mass: 15218.087 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P25515 #5: Protein | | Mass: 6476.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q3E7B6 #6: Protein | | Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c #7: Protein | | Mass: 32854.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32366 |
-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: Vo region of the V-ATPase from Saccharomyces cerevisiae Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Molecular weight | Value: 0.3 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 Details: 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The Vo region was solubilized in amphipol A8-35 (Anatrace) |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Maxtaform |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.3 K / Details: Modified for ethane/propane |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: 70 micro meter objective aperture, illuminated area of 1.58 micro meter diameter |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 37000 X / Calibrated magnification: 64350 X / Calibrated defocus min: 800 nm / Calibrated defocus max: 3400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 21 sec. / Electron dose: 100 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4365 |
Image scans | Movie frames/image: 70 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Images were recorded in "super-resolution" mode and then resampled by Fourier cropping. | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 657975 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462842 / Algorithm: FOURIER SPACE Details: Data beyond 6 A resolution were omitted from refinement. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: phenix.real_space_refine REFINEMENT TARGET: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) MODEL TO MAP FIT. CC(ACROSS WHOLE MAP VOLUME): 0.6772 CC(ONLY ACROSS ATOMS IN THE MODEL): 0.6842 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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