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- EMDB-6081: Cryo electron tomography of gp9 minus bacteriophage T4 -

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Basic information

Entry
Database: EMDB / ID: EMD-6081
TitleCryo electron tomography of gp9 minus bacteriophage T4
Map dataSub-tomogram averaging of gp9 minus T4 phage
Sample
  • Sample: gp9 minus T4 phage
  • 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: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6081.map.gz / Format: CCP4 / Size: 26 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram averaging of gp9 minus T4 phage
Voxel sizeX=Y=Z: 7.8 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-6.55576372 - 8.38896561
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-168
Dimensions144144336
Spacing144144336
CellA: 1123.2001 Å / B: 1123.2001 Å / C: 2620.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z144144336
origin x/y/z0.0000.0000.000
length x/y/z1123.2001123.2002620.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS-72-72-168
NC/NR/NS144144336
D min/max/mean-6.5568.3890.000

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Supplemental data

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Sample components

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Entire : gp9 minus T4 phage

EntireName: gp9 minus T4 phage
Components
  • Sample: gp9 minus T4 phage
  • Virus: Enterobacteria phage T4 (virus)

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Supramolecule #1000: gp9 minus T4 phage

SupramoleculeName: gp9 minus T4 phage / 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 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Sci species strain: gp9 minus / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 °
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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: OTHER / Software - Name: IMOD, Protomo, i3, EMAN / Number subtomograms used: 1998
DetailsThe particles were manually selected from cryo-tomograms.

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