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- 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
TitleCryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state (pH 7.4, C1 symmetry)
ComponentsPlasma membrane ATPase 1
KeywordsTRANSLOCASE / P type ATPase / plasma membrane H+-ATPase / hexamer
Function / homology
Function and homology information


proton export across plasma membrane / P-type H+-exporting transporter / 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 ...proton export across plasma membrane / P-type H+-exporting transporter / 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-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transporter/ATPase, N-terminus / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / E1-E2 ATPases phosphorylation site. / P-type ATPase, cytoplasmic domain N / P-type ATPase, A domain superfamily / P-type ATPase ...P-type ATPase, subfamily IIIA / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transporter/ATPase, N-terminus / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / E1-E2 ATPases phosphorylation site. / P-type ATPase, cytoplasmic domain N / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Chem-POV / SPHINGOSINE / Plasma membrane ATPase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhao, P. / Zhao, C. / Chen, D. / Yun, C. / Li, H. / Bai, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171212 China
CitationJournal: 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
DepositionSep 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Plasma membrane ATPase 1
B: Plasma membrane ATPase 1
C: Plasma membrane ATPase 1
D: Plasma membrane ATPase 1
E: Plasma membrane ATPase 1
F: Plasma membrane ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)637,34858
Polymers598,2846
Non-polymers39,06352
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Plasma membrane ATPase 1 / Proton pump 1


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 (baker's yeast)
References: UniProt: P05030, P-type H+-exporting transporter
#2: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plasma membrane ATPase 1 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 99.6 kDa/nm / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179392 / Symmetry type: POINT

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