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- EMDB-75890: Evaluating the Volta Phase Plate for Improved Tomogram Alignment ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75890
TitleEvaluating the Volta Phase Plate for Improved Tomogram Alignment in Cryo-Electron Tomography: structure of PP7 virus-like-particle with VPP (partial dataset)
Map datamain map
Sample
  • Organelle or cellular component: HEK293T cell lysate mixed with purified proteins on functionalized EM grids
KeywordsPP7 virus-like-particle / VIRUS LIKE PARTICLE
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 7.0 Å
AuthorsHutchings J / Ji D / Ali M / Siems H / Serwas D / Paraan M / Montabana EA / Yu Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: Evaluating the Volta Phase Plate for Improved Tomogram Alignment in Cryo-Electron Tomography
Authors: Hutchings J / Ji D / Zheng S / Montabana EA / Ermel UH / Peck A / Schwartz J / Woldeyes R / Paraan M / Ali M / Hill NS / Siems H / Serwas D / Cheng A / Kimanius D / Agard DA / Potter CS / Carragher B / Yu Y
History
DepositionMar 6, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75890.png

Downloads & links

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Map

FileDownload / File: emd_75890.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 352 pix.
= 531.52 Å		1.51 Å/pix.
x 352 pix.
= 531.52 Å		1.51 Å/pix.
x 352 pix.
= 531.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0011
Minimum - Maximum-0.0017032312 - 0.0031718072
Average (Standard dev.)0.000008776545 (±0.00022327356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 531.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75890_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_75890_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_75890_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 : HEK293T cell lysate mixed with purified proteins on functionalize...

EntireName: HEK293T cell lysate mixed with purified proteins on functionalized EM grids
Components
  • Organelle or cellular component: HEK293T cell lysate mixed with purified proteins on functionalized EM grids

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Supramolecule #1: HEK293T cell lysate mixed with purified proteins on functionalize...

SupramoleculeName: HEK293T cell lysate mixed with purified proteins on functionalized EM grids
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293T

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: TFS FALCON 4i (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: 0.9 µm / Nominal defocus min: 0.7000000000000001 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: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5)
Details: Initial low-resolution alignment against the same model. All subsequent high-resolution refinements are independent.
Number subtomograms used: 270
ExtractionNumber tomograms: 80 / Number images used: 270 / 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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