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- EMDB-21349: Mammalian V-ATPase from rat brain membrane-embedded Vo region rot... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21349 | |||||||||
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Title | Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) | |||||||||
![]() | Mammalian rat brain V-ATPase with SidK bound, focused refinement of the membrane embedded VO region conformational state 2 | |||||||||
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Function / homology | ![]() Metabolism of Angiotensinogen to Angiotensins / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 | ![]() | 98.9 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vqgMC ![]() 6vq6C ![]() 6vq7C ![]() 6vq8C ![]() 6vq9C ![]() 6vqaC ![]() 6vqbC ![]() 6vqcC ![]() 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 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ![]() |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 43.0 e/Å2 |
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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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 74789 |