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- EMDB-23123: Subtomogram average of the hexameric fungal plasma membrane proto... -

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Basic information

Entry
Database: EMDB / ID: EMD-23123
TitleSubtomogram average of the hexameric fungal plasma membrane proton pump Pma1 from protoplast membrane of Candida glabrata KH238 strain
Map dataPlasma membrane proton pump Pma1 from Candida glabrata KH238 strain protoplast membrane
Sample
  • Complex: Plasma membrane ATPase Pma1
Keywordshexamer / complex / MEMBRANE PROTEIN
Biological species[Candida] glabrata (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 14.0 Å
AuthorsJiang J / Chen M / Jimenez-Ortigosa C / Perlin DS / Dai W
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109025 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P011030036319 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116789-01A1 United States
CitationJournal: J Fungi (Basel) / Year: 2021
Title: Cryo-Electron Tomography of Candida glabrata Plasma Membrane Proteins.
Authors: Cristina Jiménez-Ortigosa / Jennifer Jiang / Muyuan Chen / Xuyuan Kuang / Kelley R Healey / Paul Castellano / Nikpreet Boparai / Steven J Ludtke / David S Perlin / Wei Dai /
Abstract: Fungal plasma membrane proteins have long been recognized as targets for the development of antifungal agents. Despite recent progress in experimental approaches and computational structural ...Fungal plasma membrane proteins have long been recognized as targets for the development of antifungal agents. Despite recent progress in experimental approaches and computational structural predictions, our knowledge of the structural dynamics and spatial distribution of these membrane proteins in the context of their native lipid environment remains limited. By applying cryo-electron tomography (cryoET) and subtomogram analysis, we aim to characterize the structural characteristics and spatial distribution of membrane proteins present in plasma membranes. This study has resulted in the identification of the membrane-embedded structure of the fungal H+-ATPase, Pma1. Tomograms of the plasma membrane revealed that Pma1 complexes are heterogeneously distributed as hexamers that cluster into distinct membrane microdomains. This study characterizes fungal membrane proteins in the native cellular landscape and highlights the unique potential of cryoET to advance our understanding of cellular biology and biological systems.
History
DepositionDec 16, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.36
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23123.png

Downloads & links

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Map

FileDownload / File: emd_23123.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasma membrane proton pump Pma1 from Candida glabrata KH238 strain protoplast membrane
Voxel sizeX=Y=Z: 2.727 Å
Density
Contour LevelBy AUTHOR: 2.36 / Movie #1: 2.36
Minimum - Maximum-39.005580000000002 - 38.263260000000002
Average (Standard dev.)0.04198612 (±0.9999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-84-84
Dimensions168168168
Spacing168168168
CellA=B=C: 458.136 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.7272.7272.727
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z458.136458.136458.136
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-39.00638.2630.042

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Supplemental data

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Sample components

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Entire : Plasma membrane ATPase Pma1

EntireName: Plasma membrane ATPase Pma1
Components
  • Complex: Plasma membrane ATPase Pma1

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Supramolecule #1: Plasma membrane ATPase Pma1

SupramoleculeName: Plasma membrane ATPase Pma1 / type: complex / ID: 1 / Parent: 0
Details: On protoplast membranes isolated from Candida glabrata
Source (natural)Organism: [Candida] glabrata (fungus) / Strain: KH238
Molecular weightTheoretical: 590 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 49000
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 272 / Number images used: 5108 / Software - Name: EMAN2
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 5108

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