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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: To Be Published
Title: Structural and Biophysical Dynamics of Fungal Plasma Membrane Proteins and Implications for Echinocandin Action in Candida glabrata
Authors: Jiang J / Keniya MV / Puri A / Zhan X / Cheng J / Wang H / Lin G / Lee YK / Jaber N / Hassoun Y / Shor E / Shi Z / Lee SH / Xu M / Perlin DS / Dai W
History
DepositionMay 28, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing 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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