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- EMDB-6079: Cryo electron tomography of fiberless bacteriophage T4 -

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Basic information

Entry
Database: EMDB / ID: EMD-6079
TitleCryo electron tomography of fiberless bacteriophage T4
Map dataSub-tomogram averaging of fiberless T4 phage
Sample
  • Sample: Fiberless (X4E mutant) bacteriophage T4
  • Virus: Enterobacteria phage T4 (virus)
KeywordsBacteriophage T4 / viral infection / phage-host interaction / infection initiation
Biological speciesEnterobacteria phage T4 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 31.0 Å
AuthorsHu B / Margolin W / Molineux IJ / Liu J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural remodeling of bacteriophage T4 and host membranes during infection initiation.
Authors: Bo Hu / William Margolin / Ian J Molineux / Jun Liu /
Abstract: The first stages of productive bacteriophage infections of bacterial host cells require efficient adsorption to the cell surface followed by ejection of phage DNA into the host cytoplasm. To achieve ...The first stages of productive bacteriophage infections of bacterial host cells require efficient adsorption to the cell surface followed by ejection of phage DNA into the host cytoplasm. To achieve this goal, a phage virion must undergo significant structural remodeling. For phage T4, the most obvious change is the contraction of its tail. Here, we use skinny E. coli minicells as a host, along with cryo-electron tomography and mutant phage virions, to visualize key structural intermediates during initiation of T4 infection. We show for the first time that most long tail fibers are folded back against the tail sheath until irreversible adsorption, a feature compatible with the virion randomly walking across the cell surface to find an optimal site for infection. Our data confirm that tail contraction is triggered by structural changes in the baseplate, as intermediates were found with remodeled baseplates and extended tails. After contraction, the tail tube penetrates the host cell periplasm, pausing while it degrades the peptidoglycan layer. Penetration into the host cytoplasm is accompanied by a dramatic local outward curvature of the cytoplasmic membrane as it fuses with the phage tail tip. The baseplate hub protein gp27 and/or the ejected tape measure protein gp29 likely form the transmembrane channel for viral DNA passage into the cell cytoplasm. Building on the wealth of prior biochemical and structural information, this work provides new molecular insights into the mechanistic pathway of T4 phage infection.
History
DepositionSep 1, 2014-
Header (metadata) releaseOct 1, 2014-
Map releaseAug 19, 2015-
UpdateSep 9, 2015-
Current statusSep 9, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6079.gif

Downloads & links

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Map

FileDownload / File: emd_6079.map.gz / Format: CCP4 / Size: 29.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram averaging of fiberless T4 phage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.8 Å/pix.
x 380 pix.
= 2964. Å		7.8 Å/pix.
x 144 pix.
= 1123.2 Å		7.8 Å/pix.
x 144 pix.
= 1123.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-7.03727913 - 9.29464149
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-190
Dimensions144144380
Spacing144144380
CellA: 1123.2001 Å / B: 1123.2001 Å / C: 2964.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z144144380
origin x/y/z0.0000.0000.000
length x/y/z1123.2001123.2002964.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS-72-72-190
NC/NR/NS144144380
D min/max/mean-7.0379.295-0.000

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Supplemental data

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Sample components

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Entire : Fiberless (X4E mutant) bacteriophage T4

EntireName: Fiberless (X4E mutant) bacteriophage T4
Components
  • Sample: Fiberless (X4E mutant) bacteriophage T4
  • Virus: Enterobacteria phage T4 (virus)

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Supramolecule #1000: Fiberless (X4E mutant) bacteriophage T4

SupramoleculeName: Fiberless (X4E mutant) bacteriophage T4 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Details: fiberless mutant / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Sci species strain: X4E mutant / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2, 0.1 M NaCl
GridDetails: 200 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: HOMEMADE PLUNGER / Method: Blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
DetailsWeak beam illumination
DateMar 1, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 23000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were manually selected from cryo-tomograms.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: OTHER / Software - Name: IMOD, Protomo, i3, EMAN / Number subtomograms used: 2749

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