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- EMDB-44782: D5E cage of PP7-AY-PP7: Pseudomonas phage PP7 coat protein dimer -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-44782
TitleD5E cage of PP7-AY-PP7: Pseudomonas phage PP7 coat protein dimer
Map datasharpened b-factor: -66.5
Sample
  • Complex: D5E cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 bacteriophage protein expressed in E.coli
KeywordsVLP / PP7 / coat protein dimer / cage / C2 symmetry / VIRUS LIKE PARTICLE
Biological speciesPepevirus rubrum
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsKopylov M / Hernandez C / Bobe D / Keshavarz-Joud P / Finn MG
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: Pleomorphism in wild-type and engineered PP7 virus-like particles
Authors: Keshavarz-Joud P / Kopylov M / Zhao L / Hernandez C / Bobe D / Paraan M / Finn MG
History
DepositionMay 8, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44782.png

Downloads & links

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Map

FileDownload / File: emd_44782.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened b-factor: -66.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 512 pix.
= 554.496 Å		1.08 Å/pix.
x 512 pix.
= 554.496 Å		1.08 Å/pix.
x 512 pix.
= 554.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.149
Minimum - Maximum-0.4062764 - 0.80219346
Average (Standard dev.)0.000035381272 (±0.03819487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 554.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44782_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half a

Fileemd_44782_half_map_1.map
Annotationhalf a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half b

Fileemd_44782_half_map_2.map
Annotationhalf b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : D5E cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 ba...

EntireName: D5E cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 bacteriophage protein expressed in E.coli
Components
  • Complex: D5E cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 bacteriophage protein expressed in E.coli

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Supramolecule #1: D5E cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 ba...

SupramoleculeName: D5E cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 bacteriophage protein expressed in E.coli
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pepevirus rubrum

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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 / Component - Concentration: 0.1 M / Component - Name: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10515
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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