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Yorodumi- PDB-7vh5: Cryo-EM structure of the hexameric plasma membrane H+-ATPase in t... -
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-Basic information
Entry | Database: PDB / ID: 7vh5 | ||||||
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Title | Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state (pH 7.4, C1 symmetry) | ||||||
Components | Plasma membrane ATPase 1 | ||||||
Keywords | TRANSLOCASE / P type ATPase / plasma membrane H+-ATPase / hexamer | ||||||
Function / homology | Function and homology information eisosome / P-type H+-exporting transporter / proton export across plasma membrane / P-type ion transporter activity / P-type proton-exporting transporter activity / proteasome storage granule assembly / positive regulation of TORC1 signaling / proton transmembrane transport / monoatomic ion transmembrane transport / regulation of intracellular pH ...eisosome / P-type H+-exporting transporter / proton export across plasma membrane / P-type ion transporter activity / P-type proton-exporting transporter activity / proteasome storage granule assembly / positive regulation of TORC1 signaling / proton transmembrane transport / monoatomic ion transmembrane transport / regulation of intracellular pH / transmembrane transport / membrane => GO:0016020 / membrane raft / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Zhao, P. / Zhao, C. / Chen, D. / Yun, C. / Li, H. / Bai, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure and activation mechanism of the hexameric plasma membrane H-ATPase. Authors: Peng Zhao / Chaoran Zhao / Dandan Chen / Caihong Yun / Huilin Li / Lin Bai / Abstract: The S. cerevisiae plasma membrane H-ATPase, Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H-ATPases, Pma1 ...The S. cerevisiae plasma membrane H-ATPase, Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H-ATPases, Pma1 assembles and functions as a hexamer, a property unique to this subfamily among the larger family of P-type ATPases. It has been unclear how Pma1 organizes the yeast membrane into MCP microdomains, or why it is that Pma1 needs to assemble into a hexamer to establish the membrane electrochemical proton gradient. Here we report a high-resolution cryo-EM study of native Pma1 hexamers embedded in endogenous lipids. Remarkably, we found that the Pma1 hexamer encircles a liquid-crystalline membrane domain composed of 57 ordered lipid molecules. The Pma1-encircled lipid patch structure likely serves as the building block of the MCP. At pH 7.4, the carboxyl-terminal regulatory α-helix binds to the phosphorylation domains of two neighboring Pma1 subunits, locking the hexamer in the autoinhibited state. The regulatory helix becomes disordered at lower pH, leading to activation of the Pma1 hexamer. The activation process is accompanied by a 6.7 Å downward shift and a 40° rotation of transmembrane helices 1 and 2 that line the proton translocation path. The conformational changes have enabled us to propose a detailed mechanism for ATP-hydrolysis-driven proton pumping across the plasma membrane. Our structures will facilitate the development of antifungal drugs that target this essential protein. | ||||||
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 | 7vh5.cif.gz | 847.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vh5.ent.gz | 736.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/7vh5 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/7vh5 | HTTPS FTP |
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-Related structure data
Related structure data | 31986MC 7vh6C 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
#1: Protein | Mass: 99714.023 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: PMA1, YGL008C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P05030, P-type H+-exporting transporter #2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-SPH / | 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: Plasma membrane ATPase 1 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 99.6 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179392 / Symmetry type: POINT |