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Yorodumi- PDB-6vqa: Mammalian V-ATPase from rat brain soluble V1 region rotational st... -
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-Basic information
Entry | Database: PDB / ID: 6vqa | ||||||
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Title | Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement) | ||||||
Components |
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Keywords | PROTON TRANSPORT / membrane protein complex / rotary atpase | ||||||
Function / homology | Function and homology information Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / 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 / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / regulation of cellular pH / vacuolar acidification / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / cilium assembly / transmembrane transporter complex / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / secretory granule / synaptic vesicle membrane / cilium / melanosome / ATPase binding / intracellular iron ion homeostasis / endosome / apical plasma membrane / lysosomal membrane / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Abbas, Y.M. / Rubinstein, J.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Science / Year: 2020 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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Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6vqa.cif.gz | 809.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vqa.ent.gz | 655.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vqa_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6vqa_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6vqa_validation.xml.gz | 106.8 KB | Display | |
Data in CIF | 6vqa_validation.cif.gz | 167.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/6vqa ftp://data.pdbj.org/pub/pdb/validation_reports/vq/6vqa | HTTPS FTP |
-Related structure data
Related structure data | 21346MC 6vq6C 6vq7C 6vq8C 6vq9C 6vqbC 6vqcC 6vqgC 6vqhC 6vqiC 6vqjC 6vqkC 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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1 |
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-Components
-ATPase H+-transporting V1 subunit ... , 2 types, 4 molecules ABCH
#1: Protein | Mass: 68341.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D4A133 #3: Protein | | Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P503 |
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-V-type proton ATPase subunit ... , 3 types, 9 molecules DEFIJKMNO
#2: Protein | Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62815 #4: Protein | Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCU2 #5: Protein | Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q8R2H0 |
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-Protein , 1 types, 3 molecules QRS
#6: Protein | Mass: 34693.605 Da / Num. of mol.: 3 / Fragment: N-terminal fragment with 3x FLAG tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6 |
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-Non-polymers , 2 types, 2 molecules
#7: Chemical | ChemComp-ADP / |
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#8: Chemical | ChemComp-MG / |
-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: Soluble region of rat brain V-ATPase composed of subunits A, B2, D, E1, G2, and the Legionella pneumophila effector protein SidK Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Buffer solution | pH: 7 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74789 / Algorithm: BACK PROJECTION / Symmetry type: POINT |