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- EMDB-21845: The V1 region of human V-ATPase in state 1 (focused refinement) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21845 | |||||||||
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Title | The V1 region of human V-ATPase in state 1 (focused refinement) | |||||||||
![]() | The V1 region of human V-ATPase in state 1 (focused refinement) | |||||||||
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Function / homology | ![]() proton-transporting two-sector ATPase complex / Ion channel transport / intracellular pH reduction / cellular response to increased oxygen levels / ATPase-coupled ion transmembrane transporter activity / synaptic vesicle lumen acidification / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang L / Wu H | |||||||||
![]() | ![]() Title: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Authors: Longfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu / ![]() ![]() Abstract: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton ...Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V complex. We define ATP6AP1 as a structural hub for V complex assembly because it connects to multiple V subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids. | |||||||||
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 | ![]() | 16.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
Images | ![]() | 127.3 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wlzMC ![]() 6wlwC ![]() 6wm2C ![]() 6wm3C ![]() 6wm4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Unaligned multi frame micrographs of human V-ATPase in complex with SidK [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The V1 region of human V-ATPase in state 1 (focused refinement) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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 : Human V-ATPase and SidK complex
+Supramolecule #1: Human V-ATPase and SidK complex
+Supramolecule #2: Human V-ATPase
+Supramolecule #3: SidK
+Macromolecule #1: V-type proton ATPase catalytic subunit A
+Macromolecule #2: V-type proton ATPase subunit B, brain isoform
+Macromolecule #3: SidK
+Macromolecule #4: V-type proton ATPase subunit E 1
+Macromolecule #5: V-type proton ATPase subunit G 1
+Macromolecule #6: V-type proton ATPase subunit D
+Macromolecule #7: V-type proton ATPase subunit F
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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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: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1 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: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000 |