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Open data
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Basic information
Entry | Database: PDB / ID: 6wm4 | ||||||
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Title | Human V-ATPase in state 3 with SidK and ADP | ||||||
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![]() | MEMBRANE PROTEIN / pump | ||||||
Function / homology | ![]() proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / eye pigmentation / central nervous system maturation / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity ...proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / eye pigmentation / central nervous system maturation / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / 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 / osteoclast development / 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 / azurophil granule membrane / proton transmembrane transporter activity / microvillus / autophagosome membrane / regulation of MAPK cascade / ATPase activator activity / tertiary granule membrane / 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 / ATP metabolic process / axon terminus / H+-transporting two-sector ATPase / ruffle / Insulin receptor recycling / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule membrane / secretory granule / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / 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 / early endosome / lysosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / external side of plasma membrane / Golgi membrane / axon / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Wang, L. / Wu, H. / Fu, T.M. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21849MC ![]() 6wlwC ![]() 6wlzC ![]() 6wm2C ![]() 6wm3C M: map data used to model this data 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
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Assembly
Deposited unit | ![]()
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Components
-V-type proton ATPase ... , 14 types, 30 molecules ROJIHMLKSBCAEFDGNU0123456789QP
#1: Protein | Mass: 96512.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||||||||
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#2: Protein | Mass: 43999.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||||||||
#3: Protein | Mass: 26183.346 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 13781.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 68379.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P38606, H+-transporting two-sector ATPase #8: Protein | Mass: 56561.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | | Mass: 28311.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | | Mass: 13388.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | | Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | | Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | | Mass: 55949.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 3 types, 5 molecules TYZXV
#6: Protein | Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds | ||
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#9: Protein | Mass: 65505.297 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | | Mass: 39045.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars / Non-polymers , 2 types, 9 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#18: Sugar | ChemComp-NAG / #19: Chemical | ChemComp-ADP / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human V-ATPase with SidK and ADP / Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT | ||||||||||||||||||||||||
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