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- EMDB-3689: Full T5 tail containing pb2 -

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Basic information

Entry
Database: EMDB / ID: 3689
TitleFull T5 tail containing pb2
Map dataFull T5 tail
SampleFull T5 tail:
SourceEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / 6.2 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
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: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3689.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.47 Å/pix.
= 247.27 Å
100 pix
2.47 Å/pix.
= 247.27 Å
100 pix
2.47 Å/pix.
= 247.27 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4727 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.085773915 - 0.16479601
Average (Standard dev.)5.425402E-5 (0.017719919)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 247.27002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.47272.47272.4727
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z247.270247.270247.270
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0860.1650.000

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Supplemental data

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Sample components

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Entire Full T5 tail

EntireName: Full T5 tail / Number of components: 1

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Component #1: protein, Full T5 tail

ProteinName: Full T5 tail / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF

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