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- EMDB-31989: Cryo-EM structure of the hexameric plasma membrane H+-ATPase in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-31989
TitleCryo-EM structure of the hexameric plasma membrane H+-ATPase in the active state (pH 6.0, BeF3-, conformation 1, C6 symmetry)
Map data
Sample
  • Complex: Plasma membrane ATPase 1
    • Protein or peptide: Pma1
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 / E1-E2 ATPase / 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 / E1-E2 ATPase / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhao P / Zhao C / Chen D / Yun C / Li H / Bai L
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 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31989.png

Downloads & links

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Map

FileDownload / File: emd_31989.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.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.054499537 - 0.09813711
Average (Standard dev.)0.0003482552 (±0.0027999526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0540.0980.000

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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: Pma1

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Supramolecule #1: Plasma membrane ATPase 1

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

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Macromolecule #1: Pma1

MacromoleculeName: Pma1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTDTSSSSSS SSASSVSAHQ PTQEKPAKTY DDAASESSDD DDIDALIEEL QSNHGVDDED SDNDGPVAA GEARPVPEEY LQTDPSYGLT SDEVLKRRKK YGLNQMADEK ESLVVKFVMF F VGPIQFVM EAAAILAAGL SDWVDFGVIC GLLMLNAGVG FVQEFQAGSI ...String:
MTDTSSSSSS SSASSVSAHQ PTQEKPAKTY DDAASESSDD DDIDALIEEL QSNHGVDDED SDNDGPVAA GEARPVPEEY LQTDPSYGLT SDEVLKRRKK YGLNQMADEK ESLVVKFVMF F VGPIQFVM EAAAILAAGL SDWVDFGVIC GLLMLNAGVG FVQEFQAGSI VDELKKTLAN TA VVIRDGQ LVEIPANEVV PGDILQLEDG TVIPTDGRIV TEDCFLQIDQ SAITGESLAV DKH YGDQTF SSSTVKRGEG FMVVTATGDN TFVGRAAALV NKAAGGQGHF TEVLNGIGII LLVL VIATL LLVWTACFYR TNGIVRILRY TLGITIIGVP VGLPAVVTTT MAVGAAYLAK KQAIV QKLS AIESLAGVEI LCSDKTGTLT KNKLSLHEPY TVEGVSPDDL MLTACLAASR KKKGLD AID KAFLKSLKQY PKAKDALTKY KVLEFHPFDP VSKKVTAVVE SPEGERIVCV KGAPLFV LK TVEEDHPIPE DVHENYENKV AELASRGFRA LGVARKRGEG HWEILGVMPC MDPPRDDT A QTVSEARHLG LRVKMLTGDA VGIAKETCRQ LGLGTNIYNA ERLGLGGGGD MPGSELADF VENADGFAEV FPQHKYRVVE ILQNRGYLVA MTGDGVNDAP SLKKADTGIA VEGATDAARS AADIVFLAP GLSAIIDALK TSRQIFHRMY SYVVYRIALS LHLEIFLGLW IAILDNSLDI D LIVFIAIF ADVATLAIAY DNAPYSPKPV KWNLPRLWGM SIILGIVLAI GSWITLTTMF LP KGGIIQN FGAMNGIMFL QISLTENWLI FITRAAGPFW SSIPSWQLAG AVFAVDIIAT MFT LFGWWS ENWTDIVTVV RVWIWSIGIF CVLGGFYYEM STSEAFDRLM NGKPMKEKKS TRSV EDFMA AMQRVSTQHE KET

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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
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63661
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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