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Yorodumi- PDB-6vq6: Mammalian V-ATPase from rat brain - composite model of rotational... -
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-Basic information
Entry | Database: PDB / ID: 6vq6 | ||||||
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Title | Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) | ||||||
Components |
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Keywords | PROTON TRANSPORT / membrane protein complex / rotary atpase | ||||||
Function / homology | Function and homology information Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death ...Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / intracellular organelle / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / NURF complex / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / autophagosome membrane / microvillus / regulation of MAPK cascade / ATPase activator activity / MLL1 complex / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / terminal bouton / transmembrane transport / synaptic vesicle membrane / small GTPase binding / cilium / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / apical part of cell / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / nucleoplasm / ATP binding / identical protein 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: 3.9 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 | 6vq6.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6vq6.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6vq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vq6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6vq6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6vq6_validation.xml.gz | 175.5 KB | Display | |
Data in CIF | 6vq6_validation.cif.gz | 287.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/6vq6 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/6vq6 | HTTPS FTP |
-Related structure data
Related structure data | 21317MC 6vq7C 6vq8C 6vq9C 6vqaC 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 #4: 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 ... , 10 types, 24 molecules DEFGIJKLMNOacdeghijklmno
#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 #3: Protein | | Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5FVI6 #5: 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 #6: Protein | | Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50408 #7: 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 #9: Protein | | Mass: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286 #11: Protein | | Mass: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O54715 #12: Protein | | Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5M7T6 #13: Protein | | Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5EB76 #15: Protein | Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63081 |
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-Protein , 4 types, 6 molecules QRSbfp
#8: 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 #10: Protein | | Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0K022 #14: Protein | | Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D3ZIM6 #16: Protein | | Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6AXS4 |
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-Non-polymers , 2 types, 2 molecules
#17: Chemical | ChemComp-ADP / |
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#18: 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: Rat brain V-ATPase complex bound to the Legionella pneumophila effector protein SidK Type: COMPLEX / Entity ID: #1-#16 / 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
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90648 / Algorithm: BACK PROJECTION / Symmetry type: POINT |
Atomic model building | Details: Final composite model was built from focused refinement models that were built into their corresponding focused refinement maps and subsequently aligned against the overall map before ...Details: Final composite model was built from focused refinement models that were built into their corresponding focused refinement maps and subsequently aligned against the overall map before combining into the composite model. The composite model was not refined against the data. |