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Yorodumi- EMDB-21318: Mammalian V-ATPase from rat brain with the Legionella pneumophila... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21318 | |||||||||
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Title | Mammalian V-ATPase from rat brain with the Legionella pneumophila effector protein SidK - rotational state 2 non-uniform refinement | |||||||||
Map data | Mammalian rat brain V-ATPase with SidK bound, non-uniform refinement rotational state 2 | |||||||||
Sample |
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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 / transporter activator activity / Insulin receptor recycling / eye pigmentation / central nervous system maturation / 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 / transporter activator activity / Insulin receptor recycling / eye pigmentation / central nervous system maturation / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / 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 / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / intracellular organelle / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / P-type proton-exporting transporter activity / 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 / vacuolar proton-transporting V-type ATPase complex / osteoclast development / protein localization to cilium / vacuolar acidification / regulation of cellular pH / dendritic spine membrane / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / ATPase activator activity / microvillus / autophagosome membrane / regulation of MAPK cascade / MLL1 complex / cilium assembly / positive regulation of Wnt signaling pathway / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / H+-transporting two-sector ATPase / ATP metabolic process / axon terminus / ruffle / RNA endonuclease activity / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / receptor-mediated endocytosis / secretory granule / terminal bouton / cilium / small GTPase binding / transmembrane transport / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / apical part of cell / synaptic vesicle / 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 / early endosome / lysosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Abbas YM / Rubinstein JL | |||||||||
Funding support | Canada, 1 items
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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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21318.map.gz | 141.7 MB | EMDB map data format | |
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Header (meta data) | emd-21318-v30.xml emd-21318.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_21318.png | 109.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21318 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21318 | HTTPS FTP |
-Validation report
Summary document | emd_21318_validation.pdf.gz | 359.1 KB | Display | EMDB validaton report |
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Full document | emd_21318_full_validation.pdf.gz | 358.7 KB | Display | |
Data in XML | emd_21318_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21318 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21318 | HTTPS FTP |
-Related structure data
Related structure data | 6vq7MC 6vq6C 6vq8C 6vq9C 6vqaC 6vqbC 6vqcC 6vqgC 6vqhC 6vqiC 6vqjC 6vqkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21318.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mammalian rat brain V-ATPase with SidK bound, non-uniform refinement rotational state 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Mammalian rat brain V-ATPase collar and peripheral stalks state 1...
Entire | Name: Mammalian rat brain V-ATPase collar and peripheral stalks state 1 - from focused refinement |
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Components |
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-Supramolecule #1: Mammalian rat brain V-ATPase collar and peripheral stalks state 1...
Supramolecule | Name: Mammalian rat brain V-ATPase collar and peripheral stalks state 1 - from focused refinement type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 74789 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: PROJECTION MATCHING |