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- EMDB-6558: Cryo-EM of bacteriophage phi29 emptied particles fusing with lipo... -

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Basic information

Entry
Database: EMDB / ID: EMD-6558
TitleCryo-EM of bacteriophage phi29 emptied particles fusing with liposome after low pH treatment
Map datareconstruction of bacteriophage phi29 fusing with liposomes after low pH treatment
Sample
  • Sample: the tail of bacteriophage phi29 fusing with liposomes after low pH treatment
  • Virus: Bacillus phage phi29 (virus)
Keywordsbacteriophage phi29 / empty particles / tail knob protein gp9
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 34.5 Å
AuthorsXu JW / Gui M / Wang DH / Xiang Y
CitationJournal: Nature / Year: 2016
Title: The bacteriophage ϕ29 tail possesses a pore-forming loop for cell membrane penetration.
Authors: Jingwei Xu / Miao Gui / Dianhong Wang / Ye Xiang /
Abstract: Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine ...Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine that plays a central role in host cell recognition and attachment, cell wall and membrane penetration, and viral genome ejection. The mechanisms involved in the penetration of the inner host cell membrane by bacteriophage tails are not well understood. Here we describe structural and functional studies of the bacteriophage ϕ29 tail knob protein gene product 9 (gp9). The 2.0 Å crystal structure of gp9 shows that six gp9 molecules form a hexameric tube structure with six flexible hydrophobic loops blocking one end of the tube before DNA ejection. Sequence and structural analyses suggest that the loops in the tube could be membrane active. Further biochemical assays and electron microscopy structural analyses show that the six hydrophobic loops in the tube exit upon DNA ejection and form a channel that spans the lipid bilayer of the membrane and allows the release of the bacteriophage genomic DNA, suggesting that cell membrane penetration involves a pore-forming mechanism similar to that of certain non-enveloped eukaryotic viruses. A search of other phage tail proteins identified similar hydrophobic loops, which indicates that a common mechanism might be used for membrane penetration by prokaryotic viruses. These findings suggest that although prokaryotic and eukaryotic viruses use apparently very different mechanisms for infection, they have evolved similar mechanisms for breaching the cell membrane.
History
DepositionDec 15, 2015-
Header (metadata) releaseJun 1, 2016-
Map releaseJun 29, 2016-
UpdateJun 29, 2016-
Current statusJun 29, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6558.gif

Downloads & links

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Map

FileDownload / File: emd_6558.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of bacteriophage phi29 fusing with liposomes after low pH treatment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.02 Å/pix.
x 320 pix.
= 966.4 Å		3.02 Å/pix.
x 320 pix.
= 966.4 Å		3.02 Å/pix.
x 320 pix.
= 966.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-12.715674399999999 - 27.197717669999999
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 966.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.023.023.02
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z966.400966.400966.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-12.71627.1980.000

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Supplemental data

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Sample components

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Entire : the tail of bacteriophage phi29 fusing with liposomes after low p...

EntireName: the tail of bacteriophage phi29 fusing with liposomes after low pH treatment
Components
  • Sample: the tail of bacteriophage phi29 fusing with liposomes after low pH treatment
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1000: the tail of bacteriophage phi29 fusing with liposomes after low p...

SupramoleculeName: the tail of bacteriophage phi29 fusing with liposomes after low pH treatment
type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 1

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid protein, gp8

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 4.2
Details: phage in the 20mM NaCl, 10mM Tris-Cl, 10mM MgCl2 mixed with 50mM NaAc, 150mM (NH4)2SO4, 12.5mM HEPES, 50mM KCl solution
GridDetails: Quantifoild 200 mesh grid, 1.2 um x 1.3 um
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TECNAI F20
DateApr 7, 2015
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 191 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder: 626 holder / Specimen holder model: GATAN HELIUM
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 34.5 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 802

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