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- EMDB-12644: Structure of the fungal plasma membrane proton pump Pma1 in its a... -

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Basic information

Entry
Database: EMDB / ID: EMD-12644
TitleStructure of the fungal plasma membrane proton pump Pma1 in its auto-inhibited state - hexameric assembly
Map data
Sample
  • Complex: Hexameric assembly of the fungal plasma membrane proton pump in its auto-inhibited state
    • Protein or peptide: Plasma membrane ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium
Function / homology
Function and homology information


P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
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
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsHeit S / Geurts MMG / Murphy BJ / Corey R / Mills DJ / Kuehlbrandt W / Bublitz M
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Other privateThe Academy of Medical Sciences United Kingdom
Other privateFEBS United Kingdom
Other privateEPA Cephalosporin Fund (CF 346) United Kingdom
Other privateErasmus+ United Kingdom
Other privateBiochemical Society United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: Structure of the hexameric fungal plasma membrane proton pump in its autoinhibited state.
Authors: Sabine Heit / Maxwell M G Geurts / Bonnie J Murphy / Robin A Corey / Deryck J Mills / Werner Kühlbrandt / Maike Bublitz /
Abstract: The fungal plasma membrane H-ATPase Pma1 is a vital enzyme, generating a proton-motive force that drives the import of essential nutrients. Autoinhibited Pma1 hexamers in the plasma membrane of ...The fungal plasma membrane H-ATPase Pma1 is a vital enzyme, generating a proton-motive force that drives the import of essential nutrients. Autoinhibited Pma1 hexamers in the plasma membrane of starving fungi are activated by glucose signaling and subsequent phosphorylation of the autoinhibitory domain. As related P-type adenosine triphosphatases (ATPases) are not known to oligomerize, the physiological relevance of Pma1 hexamers remained unknown. We have determined the structure of hexameric Pma1 from by electron cryo-microscopy at 3.3-Å resolution, elucidating the molecular basis for hexamer formation and autoinhibition and providing a basis for structure-based drug development. Coarse-grained molecular dynamics simulations in a lipid bilayer suggest lipid-mediated contacts between monomers and a substantial protein-induced membrane deformation that could act as a proton-attracting funnel.
History
DepositionMar 19, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ny1
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12644.png

Downloads & links

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Map

FileDownload / File: emd_12644.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.0017578702 - 1.9093826
Average (Standard dev.)0.0024646712 (±0.034767818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 318.06 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z318.060318.060318.060
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0021.9090.002

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Supplemental data

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Mask #1

Fileemd_12644_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12644_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12644_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric assembly of the fungal plasma membrane proton pump in i...

EntireName: Hexameric assembly of the fungal plasma membrane proton pump in its auto-inhibited state
Components
  • Complex: Hexameric assembly of the fungal plasma membrane proton pump in its auto-inhibited state
    • Protein or peptide: Plasma membrane ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: Hexameric assembly of the fungal plasma membrane proton pump in i...

SupramoleculeName: Hexameric assembly of the fungal plasma membrane proton pump in its auto-inhibited state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neurospora crassa (fungus) / Strain: FGSC #4761

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Macromolecule #1: Plasma membrane ATPase

MacromoleculeName: Plasma membrane ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: P-type H+-exporting transporter
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 99.984359 KDa
SequenceString: MADHSASGAP ALSTNIESGK FDEKAAEAAA YQPKPKVEDD EDEDIDALIE DLESHDGHDA EEEEEEATPG GGRVVPEDML QTDTRVGLT SEEVVQRRRK YGLNQMKEEK ENHFLKFLGF FVGPIQFVME GAAVLAAGLE DWVDFGVICG LLLLNAVVGF V QEFQAGSI ...String:
MADHSASGAP ALSTNIESGK FDEKAAEAAA YQPKPKVEDD EDEDIDALIE DLESHDGHDA EEEEEEATPG GGRVVPEDML QTDTRVGLT SEEVVQRRRK YGLNQMKEEK ENHFLKFLGF FVGPIQFVME GAAVLAAGLE DWVDFGVICG LLLLNAVVGF V QEFQAGSI VDELKKTLAL KAVVLRDGTL KEIEAPEVVP GDILQVEEGT IIPADGRIVT DDAFLQVDQS ALTGESLAVD KH KGDQVFA SSAVKRGEAF VVITATGDNT FVGRAAALVN AASGGSGHFT EVLNGIGTIL LILVIFTLLI VWVSSFYRSN PIV QILEFT LAITIIGVPV GLPAVVTTTM AVGAAYLAKK KAIVQKLSAI ESLAGVEILC SDKTGTLTKN KLSLHDPYTV AGVD PEDLM LTACLAASRK KKGIDAIDKA FLKSLKYYPR AKSVLSKYKV LQFHPFDPVS KKVVAVVESP QGERITCVKG APLFV LKTV EEDHPIPEEV DQAYKNKVAE FATRGFRSLG VARKRGEGSW EILGIMPCMD PPRHDTYKTV CEAKTLGLSI KMLTGD AVG IARETSRQLG LGTNIYNAER LGLGGGGDMP GSEVYDFVEA ADGFAEVFPQ HKYNVVEILQ QRGYLVAMTG DGVNDAP SL KKADTGIAVE GSSDAARSAA DIVFLAPGLG AIIDALKTSR QIFHRMYAYV VYRIALSIHL EIFLGLWIAI LNRSLNIE L VVFIAIFADV ATLAIAYDNA PYSQTPVKWN LPKLWGMSVL LGVVLAVGTW ITVTTMYAQG ENGGIVQNFG NMDEVLFLQ ISLTENWLIF ITRANGPFWS SIPSWQLSGA IFLVDILATC FTIWGWFEHS DTSIVAVVRI WIFSFGIFCI MGGVYYILQD SVGFDNLMH GKSPKGNQKQ RSLEDFVVSL QRVSTQHEKS Q

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration2 mg/mL
BufferpH: 6.5
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 59511
FSC plot (resolution estimation)

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