|Entry||Database: EMDB / ID: EMD-31986|
|Title||Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state (pH 7.4, C1 symmetry)|
|Sample||Plasma membrane ATPase 1:|
(ligand) x 2
|Function / homology|
Function and homology information
P-type H+-exporting transporter / proton export across plasma membrane / proteasome storage granule assembly / P-type proton-exporting transporter activity / positive regulation of TORC1 signaling / proton transmembrane transport / regulation of intracellular pH / transmembrane transport / membrane raft / mitochondrion ...P-type H+-exporting transporter / proton export across plasma membrane / proteasome storage granule assembly / P-type proton-exporting transporter activity / positive regulation of TORC1 signaling / proton transmembrane transport / regulation of intracellular pH / transmembrane transport / membrane raft / mitochondrion / integral component of membrane / ATP binding / plasma membrane / metal ion binding / cytosol
Similarity search - Function
P-type ATPase, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase ...P-type ATPase, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Plasma membrane ATPase 1
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)|
|Method||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, 1 items |
|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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_31986.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.029 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Plasma membrane ATPase 1
|Entire||Name: Plasma membrane ATPase 1 / Number of Components: 4|
-Component #1: protein, Plasma membrane ATPase 1
|Protein||Name: Plasma membrane ATPase 1 / Recombinant expression: No|
|Mass||Experimental: 99.6 MDa|
|Source||Species: Saccharomyces cerevisiae (baker's yeast)|
-Component #2: protein, Plasma membrane ATPase 1
|Protein||Name: Plasma membrane ATPase 1 / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 99.714023 kDa|
|Source||Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)|
Strain: ATCC 204508 / S288c
|Source (engineered)||Expression System: Saccharomyces cerevisiae (baker's yeast)|
-Component #3: ligand, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propy...
|Ligand||Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate|
Number of Copies: 51 / Recombinant expression: No
|Mass||Theoretical: 0.760076 kDa|
-Component #4: ligand, SPHINGOSINE
|Ligand||Name: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 0.299492 kDa|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen Name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 1.6 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Imaging Mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of Projections: 179392|
|3D reconstruction||Resolution: 3.2 Å / Resolution Method: FSC 0.143 CUT-OFF|
-Atomic model buiding
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