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- PDB-6vqi: Mammalian V-ATPase from rat brain collar and peripheral stalks ro... -
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Basic information
Entry | Database: PDB / ID: 6vqi | ||||||
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Title | Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) | ||||||
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![]() | PROTON TRANSPORT / membrane protein complex / rotary atpase | ||||||
Function / homology | ![]() Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / intracellular organelle / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane ...Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / intracellular organelle / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / transmembrane transporter complex / regulation of macroautophagy / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / terminal bouton / synaptic vesicle membrane / melanosome / synaptic vesicle / apical part of cell / ATPase binding / endosome / apical plasma membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
![]() | Abbas, Y.M. / Rubinstein, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of V-ATPase from the mammalian brain. Authors: Yazan M Abbas / Di Wu / Stephanie A Bueler / Carol V Robinson / John L Rubinstein / ![]() ![]() Abstract: In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes ...In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 179 KB | Display | ![]() |
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PDB format | ![]() | 112.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21351MC ![]() 6vq6C ![]() 6vq7C ![]() 6vq8C ![]() 6vq9C ![]() 6vqaC ![]() 6vqbC ![]() 6vqcC ![]() 6vqgC ![]() 6vqhC ![]() 6vqjC ![]() 6vqkC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Protein | Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() Has ligand of interest | N | |
-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: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1. Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90648 / Algorithm: BACK PROJECTION / Symmetry type: POINT |