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- EMDB-15153: Cryo-electron tomogram of secreted particles from Apilactobacillu... -

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Basic information

Entry
Database: EMDB / ID: EMD-15153
TitleCryo-electron tomogram of secreted particles from Apilactobacillus kunkeei (TS_04)
Map data
Sample
  • Complex: Secreted nanoparticles (membrane vesicles, protein complexes) from Apilactobacillus kunkeei
KeywordsMembrane vesicles / extracellular protein complexes / UNKNOWN FUNCTION
Biological speciesApilactobacillus kunkeei (bacteria)
Methodelectron tomography / cryo EM / Resolution: 10.0923 Å
AuthorsSeeger C / Andersson SGE
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Cryo-eletron tomogram of secreted particles from Apilactobacillus kunkeei (TS_01)
Authors: Seeger C / Andersson SGE
History
DepositionJun 13, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15153.png

Downloads & links

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Map

FileDownload / File: emd_15153.map.gz / Format: CCP4 / Size: 25 MB / Type: IMAGE STORED AS SIGNED BYTE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.09 Å/pix.
x 100 pix.
= 1009.23 Å		10.09 Å/pix.
x 512 pix.
= 5167.258 Å		10.09 Å/pix.
x 512 pix.
= 5167.258 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: 10.0923 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)11.400449999999999 (±23.541235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-10
Dimensions512512100
Spacing512512100
CellA: 5167.258 Å / B: 5167.258 Å / C: 1009.23004 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Secreted nanoparticles (membrane vesicles, protein complexes) fro...

EntireName: Secreted nanoparticles (membrane vesicles, protein complexes) from Apilactobacillus kunkeei
Components
  • Complex: Secreted nanoparticles (membrane vesicles, protein complexes) from Apilactobacillus kunkeei

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Supramolecule #1: Secreted nanoparticles (membrane vesicles, protein complexes) fro...

SupramoleculeName: Secreted nanoparticles (membrane vesicles, protein complexes) from Apilactobacillus kunkeei
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Apilactobacillus kunkeei (bacteria) / Strain: A1401

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 10.0 mM / Component - Name: Phosphate buffer / Details: 10 mM phosphate buffer, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 5s.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 95.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsThe initial raw movies were aligned and dose-weight filtered using alignframes from the IMOD package
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.0923 Å / Software - Name: IMOD (ver. v4.11.6) / Number images used: 16

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