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- EMDB-77086: Characterization standard for in-situ cryo-electron tomography: s... -

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Basic information

Entry
Database: EMDB / ID: EMD-77086
TitleCharacterization standard for in-situ cryo-electron tomography: structure of PP7 virus-like-particle in E. coli from high-pressure freezing and FIB-milling (full dataset)
Map datamain map
Sample
  • Cell: E. coli overexpressing PP7 virus-like-particle
KeywordsPP7 virus-like-particle / VIRUS LIKE PARTICLE
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 3.9 Å
AuthorsAli M / Hutchings J / Montabana EA / Schwartz J / Kopylov M / Paraan M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: bioRxiv / Year: 2026
Title: Characterization Standard for Cryo-electron Tomography.
Authors: Mallak Ali / Joshua Hutchings / Tahiti Dutta / Nikki Jean / Garret Greenan / Elizabeth A Montabana / Jonathan Schwartz / M G Finn / Matthias Haury / David A Agard / Bridget Carragher / ...Authors: Mallak Ali / Joshua Hutchings / Tahiti Dutta / Nikki Jean / Garret Greenan / Elizabeth A Montabana / Jonathan Schwartz / M G Finn / Matthias Haury / David A Agard / Bridget Carragher / Mykhailo Kopylov / Mohammadreza Paraan /
Abstract: Standardized biological specimens are essential for optimizing cryoEM workflows and benchmarking instrument performance. While apoferritin fulfills this role for single-particle analysis, no ...Standardized biological specimens are essential for optimizing cryoEM workflows and benchmarking instrument performance. While apoferritin fulfills this role for single-particle analysis, no equivalent exists for cryo-electron tomography. Ribosomes are frequently used but require large datasets due to C1 symmetry and structural heterogeneity, limiting rapid optimization and standardized comparison of workflows. Here, we present PP7 virus-like particles (VLPs) overexpressed in as a scalable in situ benchmark. VLPs have high orders of symmetry enabling rapid, high-resolution validation of tomographic pipelines from minimal datasets, while their distinct structural features across low to high resolutions provide a practical resolution metric.
History
DepositionMay 7, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77086.png

Downloads & links

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Map

FileDownload / File: emd_77086.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 288 pix.
= 432. Å		1.5 Å/pix.
x 288 pix.
= 432. Å		1.5 Å/pix.
x 288 pix.
= 432. Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0064
Minimum - Maximum-0.012879493 - 0.019505976
Average (Standard dev.)-0.000000000000004 (±0.0012857735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77086_msk_1.map
Projections & Slices
AxesZYX

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Half map: half-map from refinement

Fileemd_77086_half_map_1.map
Annotationhalf-map from refinement
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map from refinement

Fileemd_77086_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
Processingsubtomogram averaging
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: 3.9 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: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number subtomograms used: 29225
ExtractionNumber tomograms: 124 / Number images used: 29225 / Software - Name: RELION (ver. 5)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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