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- EMDB-3692: T5 tail - All data combined together -

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Basic information

Entry
Database: EMDB / ID: 3692
TitleT5 tail - All data combined together
Map dataT5 tail - All data combined together
SampleT5 tail - All data combined together
SourceEscherichia coli / / bacteria /
MethodCryo EM / helical reconstruction / 6 Å resolution
AuthorsArnaud C / Effantin G / Vives C / Engilberge S / Bacia M / Boulanger P / Girard E / Schoehn G / Breyton C
CitationJournal: Nat Commun / Year: 2017
Title: Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.
Authors: Charles-Adrien Arnaud / Grégory Effantin / Corinne Vivès / Sylvain Engilberge / Maria Bacia / Pascale Boulanger / Eric Girard / Guy Schoehn / Cécile Breyton
Abstract: The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails ...The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.
DateDeposition: Apr 26, 2017 / Header (metadata) release: Jun 14, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3692.map.gz (map file in CCP4 format, 13501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
150 pix
1.64 Å/pix.
= 246. Å
150 pix
1.64 Å/pix.
= 246. Å
150 pix
1.64 Å/pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.64 Å
Density
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.042947594 - 0.10294035
Average (Standard dev.)0.0010225214 (0.009251565)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions150150150
Origin000
Limit149149149
Spacing150150150
CellA=B=C: 246 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0430.1030.001

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Supplemental data

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Sample components

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Entire T5 tail - All data combined together

EntireName: T5 tail - All data combined together / Number of components: 1

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Component #1: protein, T5 tail - All data combined together

ProteinName: T5 tail - All data combined together / Recombinant expression: No
SourceSpecies: Escherichia coli / / bacteria /
Source (engineered)Expression System: Escherichia coli / / bacteria /

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: Cryo EM
Helical parametersAxial symmetry: C3 (3 fold cyclic) / Delta z: 40.6 Å / Delta phi: 39.1 deg.
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF

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