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- EMDB-1086: Three-dimensional rearrangement of proteins in the tail of bacter... -

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Basic information

Entry
Database: EMDB / ID: EMD-1086
TitleThree-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host.
Map dataCryoEM density of the T4 tail with contracted sheath and the baseplate in the star conformation.
Sample
  • Sample: T4 phages treated with 3 M urea
  • Virus: Enterobacteria phage T4 (virus)
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral tail assembly / virus tail, baseplate / viral release from host cell / virion component / identical protein binding
Similarity search - Function
Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate wedge protein gp10 ...Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Phage tail sheath protein, beta-sandwich domain / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / 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
Similarity search - Domain/homology
Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Tail completion protein gp15 / Tail sheath protein / Baseplate wedge protein gp6 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsLeiman PG / Chipman PR / Kostyuchenko VA / Mesyanzhinov VV / Rossmann MG
CitationJournal: Cell / Year: 2004
Title: Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host.
Authors: Petr G Leiman / Paul R Chipman / Victor A Kostyuchenko / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal ...The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal to a star shape. This causes the sheath around the tail tube to contract and the tail tube to protrude from the baseplate and pierce the outer cell membrane and the cell wall before reaching the inner cell membrane for subsequent viral DNA injection. Analogously, the T4 tail can be contracted by treatment with 3 M urea. The structure of the T4 contracted tail, including the head-tail joining region, has been determined by cryo-electron microscopy to 17 A resolution. This 1200 A-long, 20 MDa structure has been interpreted in terms of multiple copies of its approximately 20 component proteins. A comparison with the metastable hexagonal baseplate of the mature virus shows that the baseplate proteins move as rigid bodies relative to each other during the structural change.
History
DepositionJun 3, 2004-
Header (metadata) releaseJun 3, 2004-
Map releaseSep 7, 2004-
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: 2.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2n
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1tja
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2fl9
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3foi
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3h3y
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1086.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density of the T4 tail with contracted sheath and the baseplate in the star conformation.
Voxel sizeX=Y=Z: 3.93285 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 2.2
Minimum - Maximum-11.223052020000001 - 14.634929659999999
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-127
Dimensions256256256
Spacing256256256
CellA=B=C: 1006.8096 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.93285156253.93285156253.9328515625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1006.8101006.8101006.810
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-20-59
NX/NY/NZ181231119
MAP C/R/S123
start NC/NR/NS-128-128-127
NC/NR/NS256256256
D min/max/mean-11.22314.6350.000

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Supplemental data

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Sample components

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Entire : T4 phages treated with 3 M urea

EntireName: T4 phages treated with 3 M urea
Components
  • Sample: T4 phages treated with 3 M urea
  • Virus: Enterobacteria phage T4 (virus)

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Supramolecule #1000: T4 phages treated with 3 M urea

SupramoleculeName: T4 phages treated with 3 M urea / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 220 MDa / Theoretical: 220 MDa / Method: Estimate

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: phage T4 / Details: treated with 3 M urea / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: phage T4
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 220 MDa / Theoretical: 220 MDa

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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

Concentration5 mg/mL
BufferpH: 7.5 / Details: H2O
GridDetails: 200 mesh cupper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
DateJan 6, 2002
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 3.93285 µm / Number real images: 100 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: theta 45 degrees, phi 180 degrees
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 1965

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: Situs v.2.0
DetailsThe components were separately fitted using Situs v.2.0
RefinementSpace: REAL
Output model

PDB-1tja:
Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail

PDB-2fl9:
Evolution of bacteriophage tails: Structure of T4 gene product 10

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

PDB-3h3y:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

PDB-3j2n:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the contracted T4 tail

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Atomic model buiding 2

Initial modelPDB ID:
SoftwareName: Situs v.2.0
DetailsThe components were separately fitted using Situs v.2.0
RefinementSpace: REAL
Output model

PDB-1tja:
Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail

PDB-2fl9:
Evolution of bacteriophage tails: Structure of T4 gene product 10

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

PDB-3h3y:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

PDB-3j2n:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the contracted T4 tail

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Atomic model buiding 3

Initial modelPDB ID:
SoftwareName: Situs v.2.0
DetailsThe components were separately fitted using Situs v.2.0
RefinementSpace: REAL
Output model

PDB-1tja:
Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail

PDB-2fl9:
Evolution of bacteriophage tails: Structure of T4 gene product 10

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

PDB-3h3y:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

PDB-3j2n:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the contracted T4 tail

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