+Open data
-Basic information
Entry | Database: PDB / ID: 7tmt | ||||||
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Title | V-ATPase from Saccharomyces cerevisiae, State 3 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / V-ATPase | ||||||
Function / homology | Function and homology information cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / 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 / proton-transporting two-sector ATPase complex, catalytic domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / protein targeting to vacuole / vacuole organization / proton-transporting V-type ATPase complex / fungal-type vacuole / cellular hyperosmotic response / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-3,5-bisphosphate binding / plant-type vacuole / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / endomembrane system / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Vasanthakumar, T. / Keon, K.A. / Bueler, S.A. / Jaskolka, M.C. / Rubinstein, J.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Coordinated conformational changes in the V complex during V-ATPase reversible dissociation. Authors: Thamiya Vasanthakumar / Kristine A Keon / Stephanie A Bueler / Michael C Jaskolka / John L Rubinstein / Abstract: Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V region that hydrolyzes ATP ...Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V region that hydrolyzes ATP and a membrane-embedded V region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V and V complexes becoming autoinhibited on disassembly and subunit C subsequently detaching from V. In yeast, assembly of the V and V regions is mediated by the regulator of the ATPase of vacuoles and endosomes (RAVE) complex through an unknown mechanism. We used cryogenic-electron microscopy of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V complex and the V complex lacking subunit C. On separation, V undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with V. Loss of subunit C allows V to match the rotational state of V, suggesting how RAVE could reassemble V and V by recruiting subunit C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tmt.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tmt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7tmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tmt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7tmt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7tmt_validation.xml.gz | 175.1 KB | Display | |
Data in CIF | 7tmt_validation.cif.gz | 288.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tmt ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tmt | HTTPS FTP |
-Related structure data
Related structure data | 26002MC 7tmmC 7tmoC 7tmpC 7tmqC 7tmrC 7tmsC 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
-Protein , 5 types, 11 molecules ACEBDFGIKbf
#1: Protein | Mass: 67796.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: B3LH69, H+-transporting two-sector ATPase #2: Protein | Mass: 57815.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q585 #3: Protein | Mass: 26508.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Y8 #10: Protein | | Mass: 29694.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53262 #14: Protein | | Mass: 9369.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C5R9 |
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-V-type proton ATPase subunit ... , 11 types, 20 molecules HJLMNOPacdeghijklmno
#4: Protein | Mass: 12738.706 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48836 #5: Protein | | Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1W2 #6: Protein | | Mass: 13479.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYF6 #7: Protein | | Mass: 44241.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTP1 #8: Protein | | Mass: 54482.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41807 #9: Protein | | Mass: 95625.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32563 #11: Protein | | Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23968 #12: Protein | | Mass: 39822.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32366 #13: Protein | | Mass: 8387.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7B6 #15: Protein | Mass: 16357.501 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25515 #16: Protein | | Mass: 17046.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32842 |
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-Non-polymers , 1 types, 1 molecules
#17: Chemical | ChemComp-ADP / |
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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: V-ATPase, State 3 / Type: COMPLEX / Details: Intact V-ATPase in State 3 from yeast V-ATPase / Entity ID: #1-#16 / Source: NATURAL |
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Molecular weight | Value: 0.99 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42558 / Symmetry type: POINT | ||||||||||||||||||||||||
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