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- EMDB-2437: Mechanism of Membranous Tunnelling Nanotube Formation in Viral Ge... -

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Basic information

Entry
Database: EMDB / ID: EMD-2437
TitleMechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery
Map dataSubtomogram averaged gate. Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. Individual volumes were subboxed from PRD1-tube particles
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: 57.0 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: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2437.png

Downloads & links

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Map

FileDownload / File: emd_2437.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaged gate. Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. Individual volumes were subboxed from PRD1-tube particles
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-2.41711402 - 3.30758119
Average (Standard dev.)-0.00628973 (±0.70539248)
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-2.4173.308-0.006

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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: The sample contained intact PRD1 particles and PRD1 particles with protruding tubes
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: PRD1
Details: PRD1 particles exhibit a tube protruding from one of the 12 vertices. 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: 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: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / 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

DetailsThe subtomograms were extracted from volumes of PRD1-tube particles. The 138 subtomograms fulfilled the > 0.4 cross-correlation criteria.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 57.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Dynamo / Number subtomograms used: 138
Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial modelPDB ID:

1w8x

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

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