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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21848 | |||||||||
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Title | Human V-ATPase in state 2 with SidK and ADP | |||||||||
![]() | Human V-ATPase in state 2 with SidK and ADP (composite map) | |||||||||
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Function / homology | ![]() proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / intracellular pH reduction / eye pigmentation / central nervous system maturation / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / rostrocaudal neural tube patterning ...proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / intracellular pH reduction / eye pigmentation / central nervous system maturation / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / 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 / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / 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 / XBP1(S) activates chaperone genes / Amino acids regulate mTORC1 / proton-transporting V-type ATPase complex / head morphogenesis / ROS and RNS production in phagocytes / protein localization to cilium / Nef Mediated CD4 Down-regulation / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / azurophil granule membrane / autophagosome membrane / proton transmembrane transporter activity / microvillus / regulation of MAPK cascade / tertiary granule membrane / ATPase activator activity / ficolin-1-rich granule membrane / positive regulation of Wnt signaling pathway / cilium assembly / RHOA GTPase cycle / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / specific granule membrane / enzyme regulator activity / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / Insulin receptor recycling / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule membrane / secretory granule / transmembrane transport / synaptic vesicle membrane / small GTPase binding / cilium / endocytosis / phagocytic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / apical part of cell / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / lysosome / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wang L / Wu H / Fu TM | |||||||||
![]() | ![]() 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 | ![]() | 165.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.3 KB 29.3 KB | Display Display | ![]() |
Images | ![]() | 59 KB | ||
Others | ![]() | 165.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 559 KB | Display | ![]() |
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Full document | ![]() | 558.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wm3MC ![]() 6wlwC ![]() 6wlzC ![]() 6wm2C ![]() 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
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Annotation | Human V-ATPase in state 2 with SidK and ADP (composite map) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: Human V-ATPase in state 2 with SidK and ADP
File | emd_21848_additional_1.map | ||||||||||||
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Annotation | Human V-ATPase in state 2 with SidK and ADP | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human V-ATPase with SidK and ADP
+Supramolecule #1: Human V-ATPase with SidK and ADP
+Macromolecule #1: V-type proton ATPase 116 kDa subunit a isoform 1
+Macromolecule #2: V-type proton ATPase subunit C 1
+Macromolecule #3: V-type proton ATPase subunit E 1
+Macromolecule #4: V-type proton ATPase subunit G 1
+Macromolecule #5: V-type proton ATPase subunit e 1
+Macromolecule #6: Ribonuclease kappa
+Macromolecule #7: V-type proton ATPase subunit S1
+Macromolecule #8: Renin receptor
+Macromolecule #9: V-type proton ATPase 21 kDa proteolipid subunit
+Macromolecule #10: V-type proton ATPase 16 kDa proteolipid subunit
+Macromolecule #11: V-type proton ATPase subunit d 1
+Macromolecule #12: V-type proton ATPase catalytic subunit A
+Macromolecule #13: V-type proton ATPase subunit B, brain isoform
+Macromolecule #14: SidK
+Macromolecule #15: V-type proton ATPase subunit D
+Macromolecule #16: V-type proton ATPase subunit F
+Macromolecule #17: V-type proton ATPase subunit H
+Macromolecule #18: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE
-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: 7.4 |
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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: 50.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |