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- EMDB-3174: P22 bacteriophage Empty Expanded Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-3174
TitleP22 bacteriophage Empty Expanded Capsid
Map dataReconstruction of bacteriophageP22 Empty Expanded Capsid
Sample
  • Sample: Bacteriophage P22 Empty Expanded Capsid
  • Virus: Enterobacteria phage P22 (virus)
KeywordsP22 / bacteriophage / GFP / beta glucosidase / virus / AFM / cryoEM / cargo / nanocage
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.5 Å
AuthorsLlauro A / Luque D / Trus BL / Edwards E / Avera J / Reguera D / Douglas T / Pablo PJ / Caston JR
CitationJournal: Nanoscale / Year: 2016
Title: Cargo-shell and cargo-cargo couplings govern the mechanics of artificially loaded virus-derived cages.
Authors: Aida Llauró / Daniel Luque / Ethan Edwards / Benes L Trus / John Avera / David Reguera / Trevor Douglas / Pedro J de Pablo / José R Castón /
Abstract: Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging ...Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging causes internal pressure that can induce destabilization. Although it is possible to pack heterologous cargoes inside virus-derived shells, little is known about the physical determinants of these artificial nanocontainers' stability. Atomic force and three-dimensional cryo-electron microscopy provided mechanical and structural information about the physical mechanisms of viral cage stabilization beyond the mere presence/absence of cargos. We analyzed the effects of cargo-shell and cargo-cargo interactions on shell stability after encapsulating two types of proteinaceous payloads. While bound cargo to the inner capsid surface mechanically reinforced the capsid in a structural manner, unbound cargo diffusing freely within the shell cavity pressurized the cages up to ∼30 atm due to steric effects. Strong cargo-cargo coupling reduces the resilience of these nanocompartments in ∼20% when bound to the shell. Understanding the stability of artificially loaded nanocages will help to design more robust and durable molecular nanocontainers.
History
DepositionSep 29, 2015-
Header (metadata) releaseJan 20, 2016-
Map releaseFeb 1, 2017-
UpdateFeb 8, 2017-
Current statusFeb 8, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3174.png

Downloads & links

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Map

FileDownload / File: emd_3174.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of bacteriophageP22 Empty Expanded Capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.32 Å/pix.
x 180 pix.
= 777.6 Å		4.32 Å/pix.
x 180 pix.
= 777.6 Å		4.32 Å/pix.
x 180 pix.
= 777.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.5 / Movie #1: 11.5
Minimum - Maximum-47.806087490000003 - 80.863166809999996
Average (Standard dev.)0.7759006 (±10.2104044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 777.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.324.324.32
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z777.600777.600777.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-47.80680.8630.776

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Supplemental data

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Sample components

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Entire : Bacteriophage P22 Empty Expanded Capsid

EntireName: Bacteriophage P22 Empty Expanded Capsid
Components
  • Sample: Bacteriophage P22 Empty Expanded Capsid
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: Bacteriophage P22 Empty Expanded Capsid

SupramoleculeName: Bacteriophage P22 Empty Expanded Capsid / type: sample / ID: 1000 / Oligomeric state: 60 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: BACTERIA(EUBACTERIA)
Host systemOrganism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / Diameter: 648 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE
Details: Samples were applied to grids, blotted and plunged into liquid ethane
GridDetails: R 2/2 Quantifoil grids
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TECNAI F20
DateDec 11, 2014
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 200 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69444 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 69444
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping & amplitude decay
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 7628

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