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- PDB-7tmo: V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tmo | ||||||
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Title | V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1 | ||||||
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![]() | HYDROLASE / V-ATPase | ||||||
Function / homology | ![]() proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex ...proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / ATP metabolic process / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / Golgi membrane / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Vasanthakumar, T. / Keon, K.A. / Bueler, S.A. / Jaskolka, M.C. / Rubinstein, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 760.3 KB | Display | ![]() |
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PDB format | ![]() | 582.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 950 KB | Display | ![]() |
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Full document | ![]() | 989.5 KB | Display | |
Data in XML | ![]() | 107.3 KB | Display | |
Data in CIF | ![]() | 174.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 25997MC ![]() 7tmmC ![]() 7tmpC ![]() 7tmqC ![]() 7tmrC ![]() 7tmsC ![]() 7tmtC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 70515.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A6L0YX77, H+-transporting two-sector ATPase #2: Protein | Mass: 57815.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-V-type proton ATPase subunit ... , 5 types, 9 molecules GIKHJLMNP
#3: Protein | Mass: 26508.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 12738.706 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | | Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 13479.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | Mass: 54482.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#8: Chemical | ChemComp-ATP / | ||
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#9: Chemical | #10: Chemical | ChemComp-ADP / | |
-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 |
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Sample preparation
Component | Name: V1 complex without subunit C, State 1 / Type: COMPLEX Details: V1 complex without subunit C in State 1 from yeast V-ATPase following dissociation Entity ID: #1-#7 / Source: NATURAL |
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Molecular weight | Value: 0.59 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64329 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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