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- EMDB-45105: Cryo-electron tomography of Candida glabrata plasma membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-45105
TitleCryo-electron tomography of Candida glabrata plasma membrane
Map dataCryo-electron tomography of Candida glabrata plasma membranes
Sample
  • Organelle or cellular component: Candida glabrata plasma membrane
Keywordsplasma membrane / MEMBRANE PROTEIN
Biological speciesNakaseomyces glabratus (fungus)
Methodelectron tomography / cryo EM
AuthorsJiang J / Keniya MV / Perlin DS / Dai W
Funding support United States, 8 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-2046180 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109025 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM139168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM134020 United States
National Science Foundation (NSF, United States)DBI-2238093 United States
Department of Energy (DOE, United States)DE-SC0019313 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147027 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21DA056322 United States
CitationJournal: Nat Commun / Year: 2025
Title: Molecular landscape of the fungal plasma membrane and implications for antifungal action.
Authors: Jennifer Jiang / Mikhail V Keniya / Anusha Puri / Xueying Zhan / Jeff Cheng / Huan Wang / Gigi Lin / Yun-Kyung Lee / Nora Jaber / Caifeng Zhao / Cynthia Pang / Yasmine Hassoun / Haiyan Zheng ...Authors: Jennifer Jiang / Mikhail V Keniya / Anusha Puri / Xueying Zhan / Jeff Cheng / Huan Wang / Gigi Lin / Yun-Kyung Lee / Nora Jaber / Caifeng Zhao / Cynthia Pang / Yasmine Hassoun / Haiyan Zheng / Erika Shor / Zheng Shi / Sang-Hyuk Lee / Min Xu / David S Perlin / Wei Dai /
Abstract: Fungal plasma membrane proteins represent key therapeutic targets for antifungal agents, yet their native structure and spatial distribution remain poorly characterized. Herein, we employ an ...Fungal plasma membrane proteins represent key therapeutic targets for antifungal agents, yet their native structure and spatial distribution remain poorly characterized. Herein, we employ an integrative approach to investigate the organization of plasma membrane protein complexes in Candida glabrata, focusing on two abundant and essential membrane proteins, the β-(1,3)-glucan synthase (GS) and the proton pump Pma1. We show that treatment with caspofungin, an echinocandin antifungal that targets GS, disrupts the native distribution of membrane protein complexes and alters membrane biophysical properties. Perturbation of the sphingolipid biosynthesis further modulates drug susceptibility, revealing that the lipid environment plays an integral role in membrane protein organization and GS-echinocandin interactions. Our work highlights the importance of characterizing membrane proteins in their native context to understand their functions and inform the development of novel antifungal therapies.
History
DepositionMay 28, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45105.png

Downloads & links

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Map

FileDownload / File: emd_45105.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomography of Candida glabrata plasma membranes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.91 Å/pix.
x 320 pix.
= 3490.56 Å		10.91 Å/pix.
x 1024 pix.
= 11169.792 Å		10.91 Å/pix.
x 1024 pix.
= 11169.792 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.908 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-19.832342000000001 - 7.941017
Average (Standard dev.)-0.00008552922 (±0.6821318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-512-512-160
Dimensions10241024320
Spacing10241024320
CellA: 11169.792 Å / B: 11169.792 Å / C: 3490.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Candida glabrata plasma membrane

EntireName: Candida glabrata plasma membrane
Components
  • Organelle or cellular component: Candida glabrata plasma membrane

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Supramolecule #1: Candida glabrata plasma membrane

SupramoleculeName: Candida glabrata plasma membrane / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: from CBS138 (wild type) cells
Source (natural)Organism: Nakaseomyces glabratus (fungus) / Strain: CBS138

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 6 nm

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 41 / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: EMAN2 / Number images used: 38
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING ONLY

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