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- EMDB-1126: The tail structure of bacteriophage T4 and its mechanism of contr... -

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Basic information

Entry
Database: EMDB / ID: EMD-1126
TitleThe tail structure of bacteriophage T4 and its mechanism of contraction.
Map dataEM density map for the extended tail of bacteriophage T4
Sample
  • Sample: native T4 phage
  • Virus: Enterobacteria phage T4 (virus)
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, baseplate / viral tail assembly / viral release from host cell / virion component
Similarity search - Function
Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Baseplate structural protein Gp9 C-terminal domain superfamily / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein ...Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Baseplate structural protein Gp9 C-terminal domain superfamily / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Baseplate protein gp9 / Tail completion protein gp15 / Tail sheath protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.0 Å
AuthorsKostyuchenko VA / Chipman PR / Leiman PG / Arisaka F / Mesyanzhinov VV / Rossmann MG
CitationJournal: Nat Struct Mol Biol / Year: 2005
Title: The tail structure of bacteriophage T4 and its mechanism of contraction.
Authors: Victor A Kostyuchenko / Paul R Chipman / Petr G Leiman / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail ...Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fibers attached to the baseplate and the collar formed by six whiskers that interact with the long tail fibers. Comparison with the structure of the contracted tail shows that tail contraction is associated with a substantial rearrangement of the domains within the sheath protein and results in shortening of the sheath to about one-third of its original length. During contraction, the tail tube extends beneath the baseplate by about one-half of its total length and rotates by 345 degrees , allowing it to cross the host's periplasmic space.
History
DepositionMay 4, 2005-
Header (metadata) releaseMay 4, 2005-
Map releaseOct 4, 2005-
UpdateApr 17, 2013-
Current statusApr 17, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2bsg
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2m
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2bsg
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3foh
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1126.gif

Downloads & links

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Map

FileDownload / File: emd_1126.map.gz / Format: CCP4 / Size: 45.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map for the extended tail of bacteriophage T4
Voxel sizeX=Y=Z: 3.97 Å
Density
Contour Level1: 1.01 / Movie #1: 1
Minimum - Maximum-2.95275 - 7.95263
Average (Standard dev.)0.0588072 (±0.532736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-90-90-190
Dimensions180180380
Spacing180180380
CellA: 714.6 Å / B: 714.6 Å / C: 1508.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.973.973.97
M x/y/z180180380
origin x/y/z0.0000.0000.000
length x/y/z714.600714.6001508.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S213
start NC/NR/NS-90-90-190
NC/NR/NS180180380
D min/max/mean-2.9537.9530.059

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Supplemental data

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Sample components

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Entire : native T4 phage

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

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Supramolecule #1000: native T4 phage

SupramoleculeName: native T4 phage / type: sample / ID: 1000 / Oligomeric state: hexameric tails bound to 5-2 capsids / Number unique components: 1

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Supramolecule #1: Enterobacteria phage T4

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

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: H20
StainingType: NEGATIVE / Details: cryo
GridDetails: 200 mesh copper grids
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateJan 10, 2003
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 89 / Bits/pixel: 12

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Image processing

CTF correctionDetails: each particle image
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER-like
Details: reconstruction done with in-house implementation of BP RP algorithm from SPIDER to support non-cubicreconstruction volumes
Number images used: 3029

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Atomic model buiding 1

Initial modelPDB ID:

1aa0

RefinementSpace: REAL
Output model

PDB-1zku:
Fitting of the gp9 structure in the EM density of bacteriophage T4 extended tail

PDB-2bsg:
The modeled structure of fibritin (gpwac) of bacteriophage T4 based on cryo-EM reconstruction of the extended tail of bacteriophage T4

PDB-3foh:
Fitting of gp18M crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 extended tail

PDB-3j2m:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the extended T4 tail

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Atomic model buiding 2

Initial modelPDB ID:

1s2e

RefinementSpace: REAL
Output model

PDB-1zku:
Fitting of the gp9 structure in the EM density of bacteriophage T4 extended tail

PDB-2bsg:
The modeled structure of fibritin (gpwac) of bacteriophage T4 based on cryo-EM reconstruction of the extended tail of bacteriophage T4

PDB-3foh:
Fitting of gp18M crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 extended tail

PDB-3j2m:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the extended T4 tail

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