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- EMDB-48236: tcBF-STEM resolved Pseudomonas phage PP7 icosahedral T3 cage -

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Basic information

Entry
Database: EMDB / ID: EMD-48236
TitletcBF-STEM resolved Pseudomonas phage PP7 icosahedral T3 cage
Map data
Sample
  • Complex: Pseudomonas phage PP7 icosahedral T3 cage
Keywords4DSTEM resolved / VIRUS LIKE PARTICLE
Biological speciesPseudomonas phage PP7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.03 Å
AuthorsYu Y / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: Nat Methods / Year: 2025
Title: Dose-efficient cryo-electron microscopy for thick samples using tilt- corrected scanning transmission electron microscopy.
Authors: Yue Yu / Katherine A Spoth / Michael Colletta / Kayla X Nguyen / Steven E Zeltmann / Xiyue S Zhang / Mohammadreza Paraan / Mykhailo Kopylov / Charlie Dubbeldam / Daniel Serwas / Hannah Siems ...Authors: Yue Yu / Katherine A Spoth / Michael Colletta / Kayla X Nguyen / Steven E Zeltmann / Xiyue S Zhang / Mohammadreza Paraan / Mykhailo Kopylov / Charlie Dubbeldam / Daniel Serwas / Hannah Siems / David A Muller / Lena F Kourkoutis /
Abstract: Cryogenic electron microscopy is a powerful tool in structural biology. In thick specimens, challenges arise as an exponentially larger fraction of the transmitted electrons lose energy from ...Cryogenic electron microscopy is a powerful tool in structural biology. In thick specimens, challenges arise as an exponentially larger fraction of the transmitted electrons lose energy from inelastic scattering and can no longer be properly focused as a result of chromatic aberrations in the post-specimen optics. Rather than filtering out the inelastic scattering at the price of reducing potential signal, as is done in energy-filtered transmission electron microscopy, we show how a dose-efficient and unfiltered image can be rapidly obtained using tilt-corrected bright-field scanning transmission electron microscopy data collected on a pixelated detector. Enhanced contrast and a 3-5× improvement in dose efficiency are observed for two-dimensional images of intact bacterial cells and large organelles using tilt-corrected bright-field scanning transmission electron microscopy compared to energy-filtered transmission electron microscopy for thicknesses beyond 500 nm. As a proof of concept for the technique's performance in structural determination, we present a single-particle analysis map at sub-nanometer resolution for a highly symmetric virus-like particle determined from 789 particles.
History
DepositionDec 10, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48236.png

Downloads & links

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Map

FileDownload / File: emd_48236.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 443.2 Å		1.39 Å/pix.
x 320 pix.
= 443.2 Å		1.39 Å/pix.
x 320 pix.
= 443.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.385 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.36590168 - 0.8189028
Average (Standard dev.)0.002021708 (±0.070352815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 443.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48236_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_48236_half_map_1.map
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Histogram (log scale)

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Half map: #1

Fileemd_48236_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pseudomonas phage PP7 icosahedral T3 cage

EntireName: Pseudomonas phage PP7 icosahedral T3 cage
Components
  • Complex: Pseudomonas phage PP7 icosahedral T3 cage

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Supramolecule #1: Pseudomonas phage PP7 icosahedral T3 cage

SupramoleculeName: Pseudomonas phage PP7 icosahedral T3 cage / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas phage PP7 (virus)
Molecular weightTheoretical: 7.5 MDa

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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

Concentration1 mg/mL
BufferpH: 7 / Details: 100 mM potassium phosphage buffer
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TITAN THEMIS
DetailsThe microscope model is FEI/Thermo Fisher Titan Themis CryoS/TEM 60-300kV.
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 128 pixel / Digitization - Dimensions - Height: 128 pixel / Average electron dose: 45.0 e/Å2 / Details: detector used: EMPAD2.0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 1.5 µm / Illumination mode: SPOT SCAN / Imaging mode: 4D-STEM / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm

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Image processing

Detailsdetector: EMPAD 2.0
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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