+Open data
-Basic information
Entry | Database: PDB / ID: 6wm3 | ||||||
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Title | Human V-ATPase in state 2 with SidK and ADP | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / V-ATPase / proton pump | ||||||
Function / homology | Function and homology information proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / eye pigmentation / central nervous system maturation / intracellular pH reduction / transporter activator activity / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / Nef Mediated CD8 Down-regulation ...proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / eye pigmentation / central nervous system maturation / intracellular pH reduction / transporter activator activity / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / Nef Mediated CD8 Down-regulation / positive regulation of transforming growth factor beta1 production / ATPase-coupled ion transmembrane transporter activity / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / Golgi lumen acidification / plasma membrane proton-transporting V-type ATPase complex / Transferrin endocytosis and recycling / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / XBP1(S) activates chaperone genes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase complex / head morphogenesis / protein localization to cilium / vacuolar acidification / ROS and RNS production in phagocytes / Nef Mediated CD4 Down-regulation / dendritic spine membrane / regulation of cellular pH / osteoclast development / azurophil granule membrane / transmembrane transporter complex / ATPase activator activity / autophagosome membrane / microvillus / regulation of MAPK cascade / tertiary granule membrane / ficolin-1-rich granule membrane / proton transmembrane transporter activity / cilium assembly / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / angiotensin maturation / regulation of macroautophagy / Metabolism of Angiotensinogen to Angiotensins / specific granule membrane / enzyme regulator activity / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / RNA endonuclease activity / ruffle / Insulin receptor recycling / proton transmembrane transport / 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 / cilium / synaptic vesicle membrane / small GTPase binding / endocytosis / phagocytic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / presynapse / 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 | Homo sapiens (human) Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Wang, L. / Wu, H. / Fu, T.M. | ||||||
Citation | Journal: Mol Cell / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wm3.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6wm3.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6wm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/6wm3 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wm3 | HTTPS FTP |
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-Related structure data
Related structure data | 21848MC 6wlwC 6wlzC 6wm2C 6wm4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-11132 (Title: Cryo-EM structures of human V-ATPase / Data size: 8.4 TB Data #1: Unaligned multi frame micrographs of human V-ATPase in complex with SidK [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-V-type proton ATPase ... , 14 types, 30 molecules ROJIHMLKSU0123456789QCABFDEGNP
#1: Protein | Mass: 96512.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q93050 | ||||||||||||||||||||||
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#2: Protein | Mass: 43999.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21283 | ||||||||||||||||||||||
#3: Protein | Mass: 26183.346 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36543 #4: Protein | Mass: 13781.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75348 #5: Protein | | Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15342 #7: Protein | | Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15904 #9: Protein | | Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99437 #10: Protein | Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27449 #11: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61421 #12: Protein | Mass: 68379.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P38606, H+-transporting two-sector ATPase #13: Protein | Mass: 56561.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21281 #15: Protein | | Mass: 28311.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5K8 #16: Protein | | Mass: 13388.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16864 #17: Protein | | Mass: 55949.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI12 |
-Protein , 3 types, 5 molecules TVZXY
#6: Protein | Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds |
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#8: Protein | Mass: 39045.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75787 |
#14: Protein | Mass: 65505.297 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / References: UniProt: Q5ZWW6 |
-Sugars / Non-polymers , 2 types, 9 molecules
#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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT | ||||||||||||||||||||||||
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