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- EMDB-8767: Cryo-EM structure of the T4 tail tube -

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Basic information

Entry
Database: EMDB / ID: EMD-8767
TitleCryo-EM structure of the T4 tail tube
Map dataEnterobacteria Phage T4 sensu lato tail tube protein gp19 filament
Sample
  • Complex: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
    • Protein or peptide: Tail tube protein gp19
KeywordsT4 tail tube / dose limit / helical reconstruction / VIRAL PROTEIN
Function / homologysymbiont genome ejection through host cell envelope, contractile tail mechanism / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / virus tail, tube / structural molecule activity / Tail tube protein gp19
Function and homology information
Biological speciesEnterobacteria phage T4 sensu lato (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZheng W / Wang F
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
Swiss National Science Foundation310030_144243 Switzerland
CitationJournal: Structure / Year: 2017
Title: Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit.
Authors: Weili Zheng / Fengbin Wang / Nicholas M I Taylor / Ricardo C Guerrero-Ferreira / Petr G Leiman / Edward H Egelman /
Abstract: The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A ...The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A single-particle reconstruction of the T4 baseplate was able to generate a 4.1 Å resolution map for the first two rings of the tube using the overall baseplate for alignment. We have now reconstructed the T4 tail tube at a resolution of 3.4 Å, more than a 1,000-fold increase in information content for the tube from 1968. We have used legacy software (Spider) to show that we can do better than the typical 2/3 Nyquist frequency. A reasonable map can be generated with only 1.5 electrons/Å using the higher dose images for alignment, but increasing the dose results in a better map, consistent with other reports that electron dose does not represent the main limitation on resolution in cryo-electron microscopy.
History
DepositionJun 15, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseAug 16, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0163
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0163
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w5f
  • Surface level: 0.0163
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5w5f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8767.png

Downloads & links

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Map

FileDownload / File: emd_8767.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnterobacteria Phage T4 sensu lato tail tube protein gp19 filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 200 pix.
= 264. Å		1.32 Å/pix.
x 100 pix.
= 132. Å		1.32 Å/pix.
x 100 pix.
= 132. 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: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0163 / Movie #1: 0.0163
Minimum - Maximum-0.04514554 - 0.059716716
Average (Standard dev.)0.002494805 (±0.006941359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-100
Dimensions100100200
Spacing100100200
CellA: 132.0 Å / B: 132.0 Å / C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z132.000132.000264.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-100
NC/NR/NS100100200
D min/max/mean-0.0450.0600.002

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Supplemental data

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Sample components

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Entire : Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament

EntireName: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
Components
  • Complex: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
    • Protein or peptide: Tail tube protein gp19

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Supramolecule #1: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament

SupramoleculeName: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterobacteria phage T4 sensu lato (virus)

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Macromolecule #1: Tail tube protein gp19

MacromoleculeName: Tail tube protein gp19 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 sensu lato (virus)
Molecular weightTheoretical: 18.479613 KDa
SequenceString:
MFVDDVTRAF ESGDFARPNL FQVEISYLGQ NFTFQCKATA LPAGIVEKIP VGFMNRKINV AGDRTFDDWT VTVMNDEAHD ARQKFVDWQ SIAAGQGNEI TGGKPAEYKK SAIVRQYARD AKTVTKEIEI KGLWPTNVGE LQLDWDSNNE IQTFEVTLAL D YWE

UniProtKB: Tail tube protein gp19

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: Gatan image filter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 40.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 18.2 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 26320
Segment selectionNumber selected: 26320 / Software - Name: EMAN2
Startup modelType of model: NONE / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-5w5f:
Cryo-EM structure of the T4 tail tube

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