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- EMDB-9010: Structure of bacteriophage P22 with trans-envelope channel in the... -

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Basic information

Entry
Database: EMDB / ID: EMD-9010
TitleStructure of bacteriophage P22 with trans-envelope channel in the Salmonella cell wall
Map dataBacteriophage P22 with trans-envelope channel in the Salmonella cell wall
Sample
  • Complex: Structure of bacteriohage P22 with trans-envelope channel in the Salmonella cell wall
Biological speciesEnterobacteria phage P22 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsLiu J / Molineux IJ / Wang CY
CitationJournal: Nat Microbiol / Year: 2019
Title: Structural dynamics of bacteriophage P22 infection initiation revealed by cryo-electron tomography.
Authors: Chunyan Wang / Jiagang Tu / Jun Liu / Ian J Molineux /
Abstract: For successful infection, bacteriophages must overcome multiple barriers to transport their genome and proteins across the bacterial cell envelope. We use cryo-electron tomography to study the ...For successful infection, bacteriophages must overcome multiple barriers to transport their genome and proteins across the bacterial cell envelope. We use cryo-electron tomography to study the infection initiation of phage P22 in Salmonella enterica serovar Typhimurium, revealing how a channel forms to allow genome translocation into the cytoplasm. Our results show free phages that initially attach obliquely to the cell through interactions between the O antigen and two of the six tailspikes; the tail needle also abuts the cell surface. The virion then orients perpendicularly and the needle penetrates the outer membrane. The needle is released and the internal head protein gp7* is ejected and assembles into an extracellular channel that extends from the gp10 baseplate to the cell surface. A second protein, gp20, is ejected and assembles into a structure that extends the extracellular channel across the outer membrane into the periplasm. Insertion of the third ejected protein, gp16, into the cytoplasmic membrane probably completes the overall trans-envelope channel into the cytoplasm. Construction of a trans-envelope channel is an essential step during infection of Gram-negative bacteria by all short-tailed phages, because such virions cannot directly deliver their genome into the cell cytoplasm.
History
DepositionJul 30, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseApr 3, 2019-
UpdateJun 5, 2019-
Current statusJun 5, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9010.png

Downloads & links

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Map

FileDownload / File: emd_9010.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage P22 with trans-envelope channel in the Salmonella cell wall
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.5 Å/pix.
x 360 pix.
= 1620. Å		4.5 Å/pix.
x 360 pix.
= 1620. Å		4.5 Å/pix.
x 360 pix.
= 1620. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.33635417 - 0.34349042
Average (Standard dev.)-0.00012472385 (±0.028513093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 1620.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.54.54.5
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z1620.0001620.0001620.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.3360.343-0.000

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Supplemental data

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Sample components

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Entire : Structure of bacteriohage P22 with trans-envelope channel in the ...

EntireName: Structure of bacteriohage P22 with trans-envelope channel in the Salmonella cell wall
Components
  • Complex: Structure of bacteriohage P22 with trans-envelope channel in the Salmonella cell wall

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Supramolecule #1: Structure of bacteriohage P22 with trans-envelope channel in the ...

SupramoleculeName: Structure of bacteriohage P22 with trans-envelope channel in the Salmonella cell wall
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Enterobacteria phage P22 (virus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 316 / Number images used: 38000
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6002

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