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- EMDB-2439: Mechanism of Membranous Tunnelling Nanotube Formation in Viral Ge... -

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Basic information

Entry
Database: EMDB / ID: EMD-2439
TitleMechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery
Map dataThis sub-tomogram averaged tube density refers to the average class-2. Before displaying it's better to apply a low-pass filter to 50 Ang and contour at 0.8sigma (where sigma is defined by the threshold level displayed by Chimera over the RMS of the map).
Sample
  • Sample: Protruding tube (average class 2) from the 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: 66.0 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: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • 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_2439.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis sub-tomogram averaged tube density refers to the average class-2. Before displaying it's better to apply a low-pass filter to 50 Ang and contour at 0.8sigma (where sigma is defined by the threshold level displayed by Chimera over the RMS of the map).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.8 Å/pix.
x 48 pix.
= 422.4 Å
8.8 Å/pix.
x 48 pix.
= 422.4 Å
8.8 Å/pix.
x 48 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.8 Å
Density
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-2.89702868 - 3.44850159
Average (Standard dev.)-0.17037711 (±0.53865904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.88.88.8
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS484848
D min/max/mean-2.8973.449-0.170

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Supplemental data

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Sample components

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Entire : Protruding tube (average class 2) from the lipid-containing bacte...

EntireName: Protruding tube (average class 2) from the lipid-containing bacteriophage PRD1
Components
  • Sample: Protruding tube (average class 2) from the lipid-containing bacteriophage PRD1
  • Virus: Enterobacteria phage PRD1 (virus)

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Supramolecule #1000: Protruding tube (average class 2) from the lipid-containing bacte...

SupramoleculeName: Protruding tube (average class 2) from the lipid-containing bacteriophage PRD1
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage PRD1

SupramoleculeName: Enterobacteria phage PRD1 / type: virus / ID: 1 / Name.synonym: bacteriophage PRD1
Details: This is the self-assembling proteo-lipid tube. 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
TemperatureMin: 80 K / Max: 105 K / Average: 99 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
Specialist opticsEnergy filter - Name: In-column Omega filter / Energy filter - Lower energy threshold: 10.0 eV / Energy filter - Upper energy threshold: 30.0 eV
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 34138 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °

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Image processing

DetailsThis class 2 is one of the 4 classes used during multi-reference alignment. Please see details in primary reference.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 66.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Dynamo / Number subtomograms used: 33

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