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- EMDB-44783: Icosahedral T=3 cage of PP7-AY-PP7: Pseudomonas phage PP7 coat pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-44783
TitleIcosahedral T=3 cage of PP7-AY-PP7: Pseudomonas phage PP7 coat protein dimer
Map data
Sample
  • Complex: Icosahedral T=3 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: 3.05 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 8, 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_44783.png

Downloads & links

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Map

FileDownload / File: emd_44783.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.7588813 - 4.2329674
Average (Standard dev.)-0.0005786631 (±0.13488515)
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_44783_msk_1.map
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Half map: half a

Fileemd_44783_half_map_1.map
Annotationhalf a
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Half map: half b

Fileemd_44783_half_map_2.map
Annotationhalf b
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Sample components

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Entire : Icosahedral T=3 cage self-assembly of PP7-AY-PP7 coat protein dim...

EntireName: Icosahedral T=3 cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 bacteriophage protein expressed in E.coli
Components
  • Complex: Icosahedral T=3 cage self-assembly of PP7-AY-PP7 coat protein dimer of PP7 bacteriophage protein expressed in E.coli

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Supramolecule #1: Icosahedral T=3 cage self-assembly of PP7-AY-PP7 coat protein dim...

SupramoleculeName: Icosahedral T=3 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118871
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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