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- EMDB-44737: WT Pseudomonas phage PP7 capped tube VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-44737
TitleWT Pseudomonas phage PP7 capped tube VLP
Map datasharpened b-factor -47
Sample
  • Complex: C5 capped tube self-assembly of wild type PP7 bacteriophage protein expressedin E.coli
KeywordsVLP / PP7 / coat / tube / VIRUS LIKE PARTICLE
Biological speciesPepevirus rubrum
Methodsingle particle reconstruction / cryo EM / Resolution: 4.24 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: Small / Year: 2025
Title: Pleomorphism in Wild-Type and Engineered PP7 Virus-Like Particles.
Authors: Parisa Keshavarz-Joud / Matthew C Jenkins / Tahiti Dutta / Liangjun Zhao / Carolina Hernandez / Daija Bobe / Mohammadreza Paraan / M G Finn / Mykhailo Kopylov /
Abstract: Virus-like particles (VLPs) find applications across many different fields, aided by their stability, capacity for large-scale production, and presumed structural homogeneity. These attributes are a ...Virus-like particles (VLPs) find applications across many different fields, aided by their stability, capacity for large-scale production, and presumed structural homogeneity. These attributes are a result of their highly efficient self-assembly, which stems from the evolutionary pressures on the natural viruses from which they are derived. It is found that VLPs based on the Leviphage PP7 assemble in an unexpectedly wide range of morphologies. The relative abundance of these structures is sensitive to small changes in the coat protein sequence. These results raise the possibility that structural plasticity may be a general property of such self-assembling structures rather than an exception.
History
DepositionMay 3, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44737.png

Downloads & links

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Map

FileDownload / File: emd_44737.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened b-factor -47
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 420 pix.
= 451.92 Å		1.08 Å/pix.
x 420 pix.
= 451.92 Å		1.08 Å/pix.
x 420 pix.
= 451.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.269
Minimum - Maximum-0.2474509 - 0.77154833
Average (Standard dev.)0.0012822143 (±0.04959241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 451.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44737_msk_1.map
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AxesZYX

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Additional map: unsharpened

Fileemd_44737_additional_1.map
Annotationunsharpened
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Half map: #1

Fileemd_44737_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_44737_half_map_2.map
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Sample components

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Entire : C5 capped tube self-assembly of wild type PP7 bacteriophage prote...

EntireName: C5 capped tube self-assembly of wild type PP7 bacteriophage protein expressedin E.coli
Components
  • Complex: C5 capped tube self-assembly of wild type PP7 bacteriophage protein expressedin E.coli

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Supramolecule #1: C5 capped tube self-assembly of wild type PP7 bacteriophage prote...

SupramoleculeName: C5 capped tube self-assembly of wild type PP7 bacteriophage protein expressedin 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 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Details: Solarus, 15W
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: 0.01 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3733
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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