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- EMDB-41917: CryoEM structure of PP7 virus-like particle from a multi-species ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41917
TitleCryoEM structure of PP7 virus-like particle from a multi-species dataset
Map dataFinal sharpened map
Sample
  • Virus: Pseudomonas phage PP7 (virus)
KeywordsPP7 VLP / icosahedral cage / multi-species / VIRUS LIKE PARTICLE
Biological speciesPseudomonas phage PP7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsKopylov M / Bobe D / Eng ET
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2024
Title: Multi-species cryoEM calibration and workflow verification standard.
Authors: Daija Bobe / Mykhailo Kopylov / Jessalyn Miller / Aaron P Owji / Edward T Eng /
Abstract: Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established ...Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. Here, a cryoEM calibration sample consisting of a mixture of compatible macromolecules is introduced that can not only be used for resolution optimization, but also provides multiple reference points for evaluating instrument performance, data quality and image-processing workflows in a single experiment. This combined test specimen provides researchers with a reference point for validating their cryoEM pipeline, benchmarking their methodologies and testing new algorithms.
History
DepositionSep 12, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41917.png

Downloads & links

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Map

FileDownload / File: emd_41917.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 526.08 Å		1.1 Å/pix.
x 480 pix.
= 526.08 Å		1.1 Å/pix.
x 480 pix.
= 526.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.639
Minimum - Maximum-1.0090529 - 2.5285237
Average (Standard dev.)0.02156632 (±0.14146268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 526.07996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41917_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_41917_half_map_1.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_41917_half_map_2.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage PP7

EntireName: Pseudomonas phage PP7 (virus)
Components
  • Virus: Pseudomonas phage PP7 (virus)

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Supramolecule #1: Pseudomonas phage PP7

SupramoleculeName: Pseudomonas phage PP7 / type: virus / ID: 1 / Parent: 0 / Details: Virus-like particles / NCBI-ID: 12023 / Sci species name: Pseudomonas phage PP7 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Molecular weightTheoretical: 2.5 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 1803
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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