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- EMDB-66008: Cryo-electron tomography of AF647-gold-conjugated W27 binding to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66008
TitleCryo-electron tomography of AF647-gold-conjugated W27 binding to E.Coli membrane blebs.
Map dataReconstructed tomogram
Sample
  • Cell: Escherichia coli
KeywordsIgA / W27 / E.coli / SHMT / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodelectron tomography / cryo EM
AuthorsEisenstein F / Furuya G / Danev R / Shinkura R
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17gm1010008 Japan
Japan Agency for Medical Research and Development (AMED)JP243fa627001 Japan
Japan Agency for Medical Research and Development (AMED)JP22zf0127009 Japan
Japan Agency for Medical Research and Development (AMED)JP25fk0210164 Japan
Japan Science and TechnologyJPMJMS2214-17 Japan
CitationJournal: To Be Published
Title: Cross-species pathogen-reactive IgA targets chemical pattern of protein
Authors: Furuya G / Usui F / Takahashi K / Nagatoishi S / Maeda R / Tamano R / Ohno T / Sasaki K / Morita N / Gao P / Eisenstein F / Kosuge H / Shirakawa M / Arai H / Danev R / Mori H / Kikkawa M / ...Authors: Furuya G / Usui F / Takahashi K / Nagatoishi S / Maeda R / Tamano R / Ohno T / Sasaki K / Morita N / Gao P / Eisenstein F / Kosuge H / Shirakawa M / Arai H / Danev R / Mori H / Kikkawa M / Sando S / Dohmae N / Hakoshima T / Sugiura Y / Tsumoto K / Shinkura R
History
DepositionAug 29, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66008.png

Downloads & links

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Map

FileDownload / File: emd_66008.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstructed tomogram
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.4 Å/pix.
x 500 pix.
= 6700. Å		13.4 Å/pix.
x 1440 pix.
= 19296. Å		13.4 Å/pix.
x 1024 pix.
= 13721.6 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: 13.4 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-608.0 - 488.0
Average (Standard dev.)2.0057595 (±17.269203000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-250
Dimensions14401024500
Spacing10241440500
CellA: 13721.6 Å / B: 19296.0 Å / C: 6700.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Tilt series

Fileemd_66008_additional_1.map
AnnotationTilt series
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia coli

EntireName: Escherichia coli (E. coli)
Components
  • Cell: Escherichia coli

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Supramolecule #1: Escherichia coli

SupramoleculeName: Escherichia coli / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW38029

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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/RHODIUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 36 / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.12) / Number images used: 36
CTF correctionSoftware - Name: IMOD (ver. 4.12) / Type: PHASE FLIPPING ONLY

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