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- EMDB-75899: Evaluating the Volta Phase Plate for Improved Tomogram Alignment ... -

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Entry
Database: EMDB / ID: EMD-75899
TitleEvaluating the Volta Phase Plate for Improved Tomogram Alignment in Cryo-Electron Tomography: structure of 70S ribosome without VPP (partial dataset)
Map datamain map
Sample
  • Cell: Mycoplasma mycoides JCVI-Syn3A (minicells)
Keywords70S ribosome / translation / RIBOSOME
Biological speciesMycoplasma mycoides (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsHutchings J / Ji D / Ali M / Paraan M / Montabana EA / Yu Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: IUCrJ / Year: 2026
Title: Evaluating the Volta phase plate for improved tomogram alignment in cryo-electron tomography.
Authors: Joshua Hutchings / Daniel Ji / Shawn Zheng / Elizabeth A Montabana / Utz H Ermel / Ariana Peck / Jonathan Schwartz / Rahel Woldeyes / Mohammadreza Paraan / Mallak Ali / Norbert S Hill / ...Authors: Joshua Hutchings / Daniel Ji / Shawn Zheng / Elizabeth A Montabana / Utz H Ermel / Ariana Peck / Jonathan Schwartz / Rahel Woldeyes / Mohammadreza Paraan / Mallak Ali / Norbert S Hill / Hannah Siems / Daniel Serwas / Anchi Cheng / Dari Kimanius / David A Agard / Clinton S Potter / Bridget Carragher / Yue Yu /
Abstract: The Volta phase plate (VPP) can enhance low-frequency phase contrast in cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), but its impact on tomogram alignment has not been ...The Volta phase plate (VPP) can enhance low-frequency phase contrast in cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), but its impact on tomogram alignment has not been systematically assessed. Using sub-2 Å single-particle analysis (SPA) and analytical contrast transfer function (CTF) modeling, we show that despite high-frequency information loss and moderate signal damping, the VPP enhances signal in low-frequency bands that are crucial for tilt-series alignment. We show that VPP tomograms exhibit increased contrast and remain higher in contrast post denoising, for thick and crowded specimens. Quantitative comparison of tomograms acquired with and without the VPP shows improved tilt-axis orientation measurements and a higher fraction of tomograms amenable to local tilt-series alignment. Although acquisition with the VPP yields lower subtomogram averaging (STA) resolution, these results show that the primary benefits of the VPP for cryo-ET are contrast enhancement and improved tilt-series alignment robustness, which are crucial for studying cellular ultrastructure and protein organization in crowded environments, where STA at moderate resolutions remains valuable.
History
DepositionMar 6, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75899.png

Downloads & links

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Map

FileDownload / File: emd_75899.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 483.2 Å		1.51 Å/pix.
x 320 pix.
= 483.2 Å		1.51 Å/pix.
x 320 pix.
= 483.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0017
Minimum - Maximum-0.0026628107 - 0.0054315985
Average (Standard dev.)0.000033662935 (±0.00043299448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 483.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75899_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: half-map from refinement

Fileemd_75899_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_75899_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 : Mycoplasma mycoides JCVI-Syn3A (minicells)

EntireName: Mycoplasma mycoides JCVI-Syn3A (minicells)
Components
  • Cell: Mycoplasma mycoides JCVI-Syn3A (minicells)

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Supramolecule #1: Mycoplasma mycoides JCVI-Syn3A (minicells)

SupramoleculeName: Mycoplasma mycoides JCVI-Syn3A (minicells) / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma mycoides (bacteria) / Strain: JCVI-Syn3A

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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
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: 2.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.6 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: 6635
ExtractionNumber tomograms: 39 / Number images used: 6635 / 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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