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- EMDB-77092: Characterization standard for in-situ cryo-electron tomography: s... -

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Basic information

Entry
Database: EMDB / ID: EMD-77092
TitleCharacterization standard for in-situ cryo-electron tomography: structure of PP7 virus-like-particle in E. coli from plunge freezing by single particle analysis
Map datamain map
Sample
  • Cell: E. coli overexpressing PP7 virus-like-particle
KeywordsPP7 virus-like-particle / VIRUS LIKE PARTICLE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsKopylov M / Ali M / Montabana EA / Paraan M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: Characterization Standard for In-situ Cryo-electron Tomography
Authors: Ali M / Hutchings J / Dutta T / Jean N / Greenan G / Montabana EA / Schwartz J / Finn MG / Haury M / Agard DA / Carragher B / Kopylov M / Paraan M
History
DepositionMay 8, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77092.png

Downloads & links

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Map

FileReleased
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 480 pix.
= 492.96 Å		1.03 Å/pix.
x 480 pix.
= 492.96 Å		1.03 Å/pix.
x 480 pix.
= 492.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.027 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0706
Minimum - Maximum-0.08045747 - 0.25464585
Average (Standard dev.)0.0003008886 (±0.014118457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 492.95996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77092_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map from refinement

Fileemd_77092_half_map_1.map
Annotationhalf-map from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map from refinement

Fileemd_77092_half_map_2.map
Annotationhalf-map from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli overexpressing PP7 virus-like-particle

EntireName: E. coli overexpressing PP7 virus-like-particle
Components
  • Cell: E. coli overexpressing PP7 virus-like-particle

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Supramolecule #1: E. coli overexpressing PP7 virus-like-particle

SupramoleculeName: E. coli overexpressing PP7 virus-like-particle / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 34368
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Cryosparc ab initio model
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 34368
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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