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- EMDB-21348: Mammalian V-ATPase from rat brain membrane-embedded Vo region rot... -
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Basic information
Entry | Database: EMDB / ID: EMD-21348 | |||||||||
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Title | Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) | |||||||||
![]() | Mammalian rat brain V-ATPase with SidK bound, focused refinement of the membrane embedded VO region conformational state 1 | |||||||||
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![]() | membrane protein complex / rotary atpase / PROTON TRANSPORT | |||||||||
Function / homology | ![]() 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 / 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 / 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 / autophagosome membrane / 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 / proton transmembrane transport / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis / terminal bouton / transmembrane transport / synaptic vesicle membrane / small GTPase binding / cilium / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / signaling receptor activity / cell body / ATPase binding / 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 / protein-containing complex / extracellular space / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Abbas YM / Rubinstein JL | |||||||||
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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 141.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
Images | ![]() | 41.8 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 546.6 KB | Display | ![]() |
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Full document | ![]() | 546.2 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vqcMC ![]() 6vq6C ![]() 6vq7C ![]() 6vq8C ![]() 6vq9C ![]() 6vqaC ![]() 6vqbC ![]() 6vqgC ![]() 6vqhC ![]() 6vqiC ![]() 6vqjC ![]() 6vqkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Mammalian rat brain V-ATPase with SidK bound, focused refinement of the membrane embedded VO region conformational state 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
+Entire : Membrane embedded region of rat brain V-ATPase composed of subuni...
+Supramolecule #1: Membrane embedded region of rat brain V-ATPase composed of subuni...
+Macromolecule #1: ATPase H+-transporting V1 subunit D
+Macromolecule #2: V-type proton ATPase subunit F
+Macromolecule #3: V-type proton ATPase 116 kDa subunit a isoform 1
+Macromolecule #4: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
+Macromolecule #5: V-type proton ATPase subunit S1
+Macromolecule #6: V-type proton ATPase subunit
+Macromolecule #7: V-type proton ATPase subunit e 2
+Macromolecule #8: Ribonuclease K
+Macromolecule #9: V-type proton ATPase 16 kDa proteolipid subunit
+Macromolecule #10: Renin receptor
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 90648 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: PROJECTION MATCHING |