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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22122 | |||||||||
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Title | Cryo-EM structure of V-ATPase from bovine brain, state 2 | |||||||||
![]() | Structure of V-ATPase from bovine brain, state 2 | |||||||||
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Function / homology | ![]() ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels ...ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / cell projection organization / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / microtubule organizing center / Neutrophil degranulation / autophagosome membrane / ATPase activator activity / positive regulation of Wnt signaling pathway / cilium assembly / regulation of macroautophagy / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / cilium / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / early endosome / lysosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / external side of plasma membrane / axon / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.79 Å | |||||||||
![]() | Wang R / Li X | |||||||||
![]() | ![]() Title: Cryo-EM structures of intact V-ATPase from bovine brain. Authors: Rong Wang / Tao Long / Abdirahman Hassan / Jin Wang / Yingyuan Sun / Xiao-Song Xie / Xiaochun Li / ![]() Abstract: The vacuolar-type H-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been ...The vacuolar-type H-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis. Here, we report two cryo-EM structures of the intact V-ATPase from bovine brain with all the subunits including the subunit H, which is essential for ATPase activity. Two type-I transmembrane proteins, Ac45 and (pro)renin receptor, along with subunit c", constitute the core of the c-ring. Three different conformations of A/B heterodimers suggest a mechanism for ATP hydrolysis that triggers a rotation of subunits DF, inducing spinning of subunit d with respect to the entire c-ring. Moreover, many lipid molecules have been observed in the Vo domain to mediate the interactions between subunit c, c", (pro)renin receptor, and Ac45. These two structures reveal unique features of mammalian V-ATPase and suggest a mechanism of V1-Vo torque transmission. | |||||||||
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 | ![]() | 468.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.5 KB 24.5 KB | Display Display | ![]() |
Images | ![]() | 45 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xbyMC ![]() 6xbwC 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 | Structure of V-ATPase from bovine brain, state 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 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 : Cryo-EM structure of V-ATPase complex from bovine brain, state 2
+Supramolecule #1: Cryo-EM structure of V-ATPase complex from bovine brain, state 2
+Macromolecule #1: V-type proton ATPase catalytic subunit A
+Macromolecule #2: V-type proton ATPase subunit B, brain isoform
+Macromolecule #3: V-type proton ATPase subunit C 1
+Macromolecule #4: V-type proton ATPase subunit D
+Macromolecule #5: V-type proton ATPase subunit E 1
+Macromolecule #6: V-type proton ATPase subunit F
+Macromolecule #7: V-type proton ATPase subunit G
+Macromolecule #8: V-type proton ATPase subunit H
+Macromolecule #9: V-type proton ATPase subunit a
+Macromolecule #10: V-type proton ATPase 21 kDa proteolipid subunit
+Macromolecule #11: V-type proton ATPase subunit d 1
+Macromolecule #12: V-type proton ATPase 16 kDa proteolipid subunit
+Macromolecule #13: V-type proton ATPase subunit S1
+Macromolecule #14: Renin receptor
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #17: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
+Macromolecule #18: 2-acetamido-2-deoxy-beta-D-glucopyranose
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41821 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |