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- EMDB-64795: CryoEM map of TenpIN typeIII toxin-antitoxin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64795
TitleCryoEM map of TenpIN typeIII toxin-antitoxin complex
Map data
Sample
  • Complex: TenpIN toxin-antitoxin complex from Escherichia coli
KeywordsType III TA system / Cryo-EM SPA / TenpIN / Ribonucleoprotein (RNP) complex. / RNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsNadig K / Padmanabhan P / Dutta S / Singh M
Funding support India, 3 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR56485/BMS/85/598/2024 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
CitationJournal: To Be Published
Title: CryoEM map of TenpIN typeIII toxin-antitoxin complex
Authors: Nadig K / Padmanabhan P / Dutta S / Singh M
History
DepositionMay 26, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64795.png

Downloads & links

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Map

FileDownload / File: emd_64795.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 220 pix.
= 202.4 Å		0.92 Å/pix.
x 220 pix.
= 202.4 Å		0.92 Å/pix.
x 220 pix.
= 202.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0276
Minimum - Maximum-0.06980453 - 0.11569341
Average (Standard dev.)0.000020788902 (±0.0038300361)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 202.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64795_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64795_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TenpIN toxin-antitoxin complex from Escherichia coli

EntireName: TenpIN toxin-antitoxin complex from Escherichia coli
Components
  • Complex: TenpIN toxin-antitoxin complex from Escherichia coli

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Supramolecule #1: TenpIN toxin-antitoxin complex from Escherichia coli

SupramoleculeName: TenpIN toxin-antitoxin complex from Escherichia coli / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ETEC1722

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 327240
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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