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- EMDB-5528: Cryo-EM structure of the contracted bacteriophage T4 tail contain... -

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Basic information

Entry
Database: EMDB / ID: EMD-5528
TitleCryo-EM structure of the contracted bacteriophage T4 tail containing the collar and whiskers made of fibritin molecules.
Map dataCryo-EM reconstruction of the contracted T4 tail containing the collar and whiskers
Sample
  • Sample: bacteriophage T4Escherichia virus T4
  • Virus: Enterobacteria phage T4 (virus)
Keywordsbacteriophage / T4 / phage / collar / whiskers / fibritin
Function / homologyFibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsFokine A / Zhang Z / Kanamaru S / Bowman VD / Aksyuk AA / Arisaka F / Rao VB / Rossmann MG
CitationJournal: J Mol Biol / Year: 2013
Title: The molecular architecture of the bacteriophage T4 neck.
Authors: Andrei Fokine / Zhihong Zhang / Shuji Kanamaru / Valorie D Bowman / Anastasia A Aksyuk / Fumio Arisaka / Venigalla B Rao / Michael G Rossmann /
Abstract: A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently ...A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently assembled head. Here we report the crystal structure of the gp15 hexamer, describe its interactions in T4 virions that have either an extended tail or a contracted tail, and discuss its structural relationship to other phage proteins. The neck of T4 virions is decorated by the "collar" and "whiskers", made of fibritin molecules. Fibritin acts as a chaperone helping to attach the long tail fibers to the virus during the assembly process. The collar and whiskers are environment-sensing devices, regulating the retraction of the long tail fibers under unfavorable conditions, thus preventing infection. Cryo-electron microscopy analysis suggests that twelve fibritin molecules attach to the phage neck with six molecules forming the collar and six molecules forming the whiskers.
History
DepositionNov 2, 2012-
Header (metadata) releaseDec 5, 2012-
Map releaseMar 6, 2013-
UpdateMay 15, 2013-
Current statusMay 15, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2o
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2o
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5528_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5528.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the contracted T4 tail containing the collar and whiskers
Voxel sizeX=Y=Z: 3.572 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-7.67521191 - 11.692408560000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-125
Dimensions250250250
Spacing250250250
CellA=B=C: 893.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.5723.5723.572
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z893.000893.000893.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
D min/max/mean-7.67511.692-0.000

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Supplemental data

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Sample components

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Entire : bacteriophage T4

EntireName: bacteriophage T4 (virus)
Components
  • Sample: bacteriophage T4Escherichia virus T4
  • Virus: Enterobacteria phage T4 (virus)

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Supramolecule #1000: bacteriophage T4

SupramoleculeName: bacteriophage T4 / type: sample / ID: 1000 / Details: The phage tails were contracted using 4M urea. / Number unique components: 1

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: Enterobacteria phage T4 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Enterobacteria phage T4
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 50 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 8 mM MgCl2
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39190 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 38000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateMar 7, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 97 / Average electron dose: 16 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: phase flipping
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: The reconstruction of the contracted T4 tail which lacked the collar and whiskers (EMDB accession code 1086; Leiman et al., 2004, Cell 118, 419-429) was used as the initial model.
Number images used: 2727

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