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- EMDB-31986: Cryo-EM structure of the hexameric plasma membrane H+-ATPase in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-31986
TitleCryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state (pH 7.4, C1 symmetry)
Map data
Sample
  • Complex: Plasma membrane ATPase 1
    • Protein or peptide: Plasma membrane ATPase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: SPHINGOSINE
KeywordsP type ATPase / plasma membrane H+-ATPase / hexamer / TRANSLOCASE
Function / homology
Function and homology information


P-type H+-exporting transporter / eisosome / 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 ...P-type H+-exporting transporter / eisosome / 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 / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / plasma membrane / 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 actuator domain / 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, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase actuator domain / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Plasma membrane ATPase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhao P / Zhao C
Funding support China, 1 items
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, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vh5
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31986.png

Downloads & links

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Map

FileDownload / File: emd_31986.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 300 pix.
= 308.7 Å		1.03 Å/pix.
x 300 pix.
= 308.7 Å		1.03 Å/pix.
x 300 pix.
= 308.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.11024213 - 0.18516795
Average (Standard dev.)0.0004131027 (±0.0055025974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 308.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z308.700308.700308.700
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1100.1850.000

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Supplemental data

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Sample components

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Entire : Plasma membrane ATPase 1

EntireName: Plasma membrane ATPase 1
Components
  • Complex: Plasma membrane ATPase 1
    • Protein or peptide: Plasma membrane ATPase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: SPHINGOSINE

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Supramolecule #1: Plasma membrane ATPase 1

SupramoleculeName: Plasma membrane ATPase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 99.6 kDa/nm

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Macromolecule #1: Plasma membrane ATPase 1

MacromoleculeName: Plasma membrane ATPase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: P-type H+-exporting transporter
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 99.714023 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTDTSSSSSS SSASSVSAHQ PTQEKPAKTY DDAASESSDD DDIDALIEEL QSNHGVDDED SDNDGPVAAG EARPVPEEYL QTDPSYGLT SDEVLKRRKK YGLNQMADEK ESLVVKFVMF FVGPIQFVME AAAILAAGLS DWVDFGVICG LLMLNAGVGF V QEFQAGSI ...String:
MTDTSSSSSS SSASSVSAHQ PTQEKPAKTY DDAASESSDD DDIDALIEEL QSNHGVDDED SDNDGPVAAG EARPVPEEYL QTDPSYGLT SDEVLKRRKK YGLNQMADEK ESLVVKFVMF FVGPIQFVME AAAILAAGLS DWVDFGVICG LLMLNAGVGF V QEFQAGSI VDELKKTLAN TAVVIRDGQL VEIPANEVVP GDILQLEDGT VIPTDGRIVT EDCFLQIDQS AITGESLAVD KH YGDQTFS SSTVKRGEGF MVVTATGDNT FVGRAAALVN KAAGGQGHFT EVLNGIGIIL LVLVIATLLL VWTACFYRTN GIV RILRYT LGITIIGVPV GLPAVVTTTM AVGAAYLAKK QAIVQKLSAI ESLAGVEILC SDKTGTLTKN KLSLHEPYTV EGVS PDDLM LTACLAASRK KKGLDAIDKA FLKSLKQYPK AKDALTKYKV LEFHPFDPVS KKVTAVVESP EGERIVCVKG APLFV LKTV EEDHPIPEDV HENYENKVAE LASRGFRALG VARKRGEGHW EILGVMPCMD PPRDDTAQTV SEARHLGLRV KMLTGD AVG IAKETCRQLG LGTNIYNAER LGLGGGGDMP GSELADFVEN ADGFAEVFPQ HKYRVVEILQ NRGYLVAMTG DGVNDAP SL KKADTGIAVE GATDAARSAA DIVFLAPGLS AIIDALKTSR QIFHRMYSYV VYRIALSLHL EIFLGLWIAI LDNSLDID L IVFIAIFADV ATLAIAYDNA PYSPKPVKWN LPRLWGMSII LGIVLAIGSW ITLTTMFLPK GGIIQNFGAM NGIMFLQIS LTENWLIFIT RAAGPFWSSI PSWQLAGAVF AVDIIATMFT LFGWWSENWT DIVTVVRVWI WSIGIFCVLG GFYYEMSTSE AFDRLMNGK PMKEKKSTRS VEDFMAAMQR VSTQHEKET

UniProtKB: Plasma membrane ATPase 1

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 51 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179392
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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