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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
SampleT5 tail - All data combined together
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataT5 tail - All data combined together
Methodhelical reconstruction, at 6 Å resolution
AuthorsArnaud C / Effantin G / Vives C / Engilberge S / Bacia M / Boulanger P / Girard E / Schoehn G / Breyton C
CitationNat Commun, 2017, 8, 1953-1953

Nat Commun, 2017, 8, 1953-1953 Yorodumi Papers
Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.
Charles-Adrien Arnaud / Grégory Effantin / Corinne Vivès / Sylvain Engilberge / Maria Bacia / Pascale Boulanger / Eric Girard / Guy Schoehn / Cécile Breyton

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
  • Download
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Supplemental images

Downloads & links

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Map

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

Image control

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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 / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen statefilament
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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