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- EMDB-75263: Apoferritin single-particle cryo-EM reconstruction using a Volta ... -

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Entry
Database: EMDB / ID: EMD-75263
TitleApoferritin single-particle cryo-EM reconstruction using a Volta phase plate
Map data
Sample
  • Complex: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate
Keywordsapoferritin / ferritin / iron storage / protein nanocage / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsYu Y / Montabana L
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
DepositionJan 26, 2026-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75263.png

Downloads & links

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Map

FileDownload / File: emd_75263.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.29 Å/pix.
x 760 pix.
= 218.88 Å		0.29 Å/pix.
x 760 pix.
= 218.88 Å		0.29 Å/pix.
x 760 pix.
= 218.88 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.288 Å
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Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.20018142 - 0.42716855
Average (Standard dev.)-0.000059485803 (±0.017666267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions760760760
Spacing760760760
CellA=B=C: 218.87999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75263_msk_1.map
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Half map: #1

Fileemd_75263_half_map_1.map
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Half map: #2

Fileemd_75263_half_map_2.map
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Sample components

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Entire : Comparative apoferritin single-particle cryo-EM acquired with a V...

EntireName: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate
Components
  • Complex: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate

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Supramolecule #1: Comparative apoferritin single-particle cryo-EM acquired with a V...

SupramoleculeName: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate
type: complex / ID: 1 / Parent: 0
Details: This map is a single-particle cryo-EM reconstruction of apoferritin acquired using a Volta phase plate with low defocus under matched sample preparation and processing conditions. Using the ...Details: This map is a single-particle cryo-EM reconstruction of apoferritin acquired using a Volta phase plate with low defocus under matched sample preparation and processing conditions. Using the same number of particles (300,702), the final reconstruction reached a global resolution of 1.90 angstrom.
Source (natural)Organism: Mus musculus (house mouse)

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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

Concentration19 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 300702
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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