+Open data
-Basic information
Entry | Database: PDB / ID: 6xby | ||||||
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Title | Cryo-EM structure of V-ATPase from bovine brain, state 2 | ||||||
Components |
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Keywords | PROTON TRANSPORT | ||||||
Function / homology | Function and homology information 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 / ATPase binding / signaling receptor activity / postsynaptic membrane / intracellular iron ion homeostasis / endosome / endosome membrane / early endosome / lysosome / 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 | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.79 Å | ||||||
Authors | Wang, R. / Li, X. | ||||||
Citation | Journal: Nat Commun / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xby.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6xby.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6xby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xby_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6xby_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6xby_validation.xml.gz | 173.5 KB | Display | |
Data in CIF | 6xby_validation.cif.gz | 276.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xby ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xby | HTTPS FTP |
-Related structure data
Related structure data | 22122MC 6xbwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-V-type proton ATPase ... , 13 types, 29 molecules ABCDEFGHIJKLMNOPabdqpcgklmnos
#1: Protein | Mass: 68420.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P31404, H+-transporting two-sector ATPase #2: Protein | Mass: 56637.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31408 #3: Protein | | Mass: 44042.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P21282 #4: Protein | | Mass: 28297.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3Q1M4W9, UniProt: P39942*PLUS #5: Protein | Mass: 26178.371 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P11019 #6: Protein | | Mass: 13417.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28029 #7: Protein | Mass: 13588.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q0VCV6 #8: Protein | | Mass: 54155.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MZL6 #9: Protein | | Mass: 96431.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MJV0, UniProt: Q29466*PLUS #10: Protein | | Mass: 21530.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA24 #11: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61420 #12: Protein | Mass: 15727.726 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23956 #13: Protein | | Mass: 51818.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P40682 |
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-Protein / Sugars , 2 types, 7 molecules r
#14: Protein | Mass: 39529.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81134 |
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#18: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 9 molecules
#15: Chemical | ChemComp-MG / |
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#16: Chemical | ChemComp-ADP / |
#17: Chemical | ChemComp-POV / ( |
-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: Cryo-EM structure of V-ATPase complex from bovine brain, state 2 Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL |
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Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 7.5 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41821 / Symmetry type: POINT |