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- EMDB-3548: Putative initial stage of viral DNA ejection in membrane-containi... -

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Basic information

Entry
Database: EMDB / ID: EMD-3548
TitlePutative initial stage of viral DNA ejection in membrane-containing bacteriophage PRD1
Map dataPlease open in Imagej or Amira
Sample
  • Virus: Enterobacteria phage PRD1 (virus)
Biological speciesEnterobacteria phage PRD1 (virus)
Methodelectron tomography / cryo EM
AuthorsAbrescia NGA
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2017
Title: Membrane-assisted viral DNA ejection.
Authors: Isaac Santos-Pérez / Hanna M Oksanen / Dennis H Bamford / Felix M Goñi / David Reguera / Nicola G A Abrescia /
Abstract: Genome packaging and delivery are fundamental steps in the replication cycle of all viruses. Icosahedral viruses with linear double-stranded DNA (dsDNA) usually package their genome into a preformed, ...Genome packaging and delivery are fundamental steps in the replication cycle of all viruses. Icosahedral viruses with linear double-stranded DNA (dsDNA) usually package their genome into a preformed, rigid procapsid using the power generated by a virus-encoded packaging ATPase. The pressure and stored energy due to this confinement of DNA at a high density is assumed to drive the initial stages of genome ejection. Membrane-containing icosahedral viruses, such as bacteriophage PRD1, present an additional architectural complexity by enclosing their genome within an internal membrane vesicle. Upon adsorption to a host cell, the PRD1 membrane remodels into a proteo-lipidic tube that provides a conduit for passage of the ejected linear dsDNA through the cell envelope. Based on volume analyses of PRD1 membrane vesicles captured by cryo-electron tomography and modeling of the elastic properties of the vesicle, we propose that the internal membrane makes a crucial and active contribution during infection by maintaining the driving force for DNA ejection and countering the internal turgor pressure of the host. These novel functions extend the role of the PRD1 viral membrane beyond tube formation or the mere physical confinement of the genome. The presence and assistance of an internal membrane might constitute a biological advantage that extends also to other viruses that package their linear dsDNA to high density within an internal vesicle.
History
DepositionDec 20, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseJan 25, 2017-
UpdateAug 23, 2017-
Current statusAug 23, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3548.png

Downloads & links

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Map

FileDownload / File: emd_3548.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlease open in Imagej or Amira
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.8 Å/pix.
x 140 pix.
= 1232. Å		8.8 Å/pix.
x 140 pix.
= 1232. Å		8.8 Å/pix.
x 140 pix.
= 1232. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.8 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-5.3951197 - 4.707943
Average (Standard dev.)-0.0011751546 (±0.97924024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 1232.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.88.88.8
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z1232.0001232.0001232.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-5.3954.708-0.001

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Supplemental data

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Additional map: Denoised volume using TOMOAND

Fileemd_3548_additional.map
AnnotationDenoised volume using TOMOAND
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage PRD1

EntireName: Enterobacteria phage PRD1 (virus)
Components
  • Virus: Enterobacteria phage PRD1 (virus)

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Supramolecule #1: Enterobacteria phage PRD1

SupramoleculeName: Enterobacteria phage PRD1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10658 / Sci species name: Enterobacteria phage PRD1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightExperimental: 66 MDa
Virus shellShell ID: 1 / Name: PRD1 / Diameter: 650.0 Å / T number (triangulation number): 25

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.2 / Component:
NameFormula
Phosphate
Magnesium ChlorideMgCl2
GridModel: QUANTIFOIL R 2/1 (or R 3.5/1) / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK III / Details: Blot for 4 seconds before plunging.
Details20 mM Phosphate Buffer 1 mM MgCl2
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion BSA gold tracer / Diameter: 10 nm

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Electron microscopy

MicroscopeJEOL 2200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 5.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 8.0 µm / Nominal magnification: 25000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 85

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