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- EMDB-2438: Mechanism of Membranous Tunnelling Nanotube Formation in Viral Ge... -

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Basic information

Entry
Database: EMDB / ID: EMD-2438
TitleMechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery
Map dataContour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
Sample
  • Sample: Lipid-containing bacteriophage PRD1
  • Virus: Enterobacteria phage PRD1 (virus)
Keywordsvirus / structural virology / viral genome delivery / proteo-lipidic structures / membrane remodelling / nanotube formation / single-particle tomography / cellular tomography
Biological speciesEnterobacteria phage PRD1 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 64.0 Å
AuthorsPeralta B / Gil-Carton D / Castano-Diez D / Bertin A / Boulogne C / Oksanen HM / Bamford DH / Abrescia NGA
CitationJournal: Nature / Year: 2004
Title: Membrane structure and interactions with protein and DNA in bacteriophage PRD1.
Authors: Joseph J B Cockburn / Nicola G A Abrescia / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / James M Benevides / George J Thomas / Jaana K H Bamford / Dennis H Bamford / David I Stuart /
Abstract: Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated ...Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 A resolution by cryo-electron microscopy and image reconstruction, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 A resolution, allows the first detailed analysis of a membrane-containing virus. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.
History
DepositionAug 13, 2013-
Header (metadata) releaseSep 11, 2013-
Map releaseOct 2, 2013-
UpdateOct 16, 2013-
Current statusOct 16, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_2438.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
Voxel sizeX=Y=Z: 8.8 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 0.7
Minimum - Maximum-2.83609939 - 3.94621778
Average (Standard dev.)-0.19220899 (±0.84541529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 844.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.88.88.8
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z844.800844.800844.800
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-2.8363.946-0.192

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Supplemental data

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Sample components

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Entire : Lipid-containing bacteriophage PRD1

EntireName: Lipid-containing bacteriophage PRD1
Components
  • Sample: Lipid-containing bacteriophage PRD1
  • Virus: Enterobacteria phage PRD1 (virus)

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Supramolecule #1000: Lipid-containing bacteriophage PRD1

SupramoleculeName: Lipid-containing bacteriophage PRD1 / type: sample / ID: 1000
Details: Please keep in mind that these are PRD1 particles with a protruding tube. Therefore the icosahedral symmetry is broken and never applied during data processing and averaging
Oligomeric state: A pseudo T=25 assembly / Number unique components: 1
Molecular weightTheoretical: 70 MDa

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Supramolecule #1: Enterobacteria phage PRD1

SupramoleculeName: Enterobacteria phage PRD1 / type: virus / ID: 1 / Name.synonym: bacteriophage PRD1
Details: Infects both Escherichia coli and Salmonella enterica
NCBI-ID: 10658 / Sci species name: Enterobacteria phage PRD1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage PRD1
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 70 MDa
Virus shellShell ID: 1 / Name: P3

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.2 / Details: 20 mM Phosphate Buffer 1 mM MgCl2
GridDetails: 200 mesh QUANTIFOIL R 2/1 (or R 3.5/1) copper grid, glow discharged in air atmosphere
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 34138 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 25000
Specialist opticsEnergy filter - Name: In-column Omega filter / Energy filter - Lower energy threshold: 10.0 eV / Energy filter - Upper energy threshold: 30.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
TemperatureMin: 80 K / Max: 105 K / Average: 99 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
DateJan 4, 2012
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: OTHER / Average electron dose: 100 e/Å2 / Bits/pixel: 16

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 64.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Dynamo / Number subtomograms used: 174
DetailsThe tube was use as pivot for initial alignment. Please see details in primary reference.

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: Chimera
DetailsFor the docking, please, see the protocol described in the primary reference
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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