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- EMDB-1414: Molecular architecture of the prolate head of bacteriophage T4. -

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Basic information

Entry
Database: EMDB / ID: EMD-1414
TitleMolecular architecture of the prolate head of bacteriophage T4.
Map dataCryo-EM reconstruction of the bacteriophage T4 prolate head using D5 symmetry
Sample
  • Sample: Bacteriophage T4 capsid
  • Virus: Enterobacteria phage T4 (virus)
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsFokine A / Chipman P / Leiman P / Mesyanzhinov V / Rao V / Rossmann M
CitationJournal: Proc Natl Acad Sci U S A / Year: 2004
Title: Molecular architecture of the prolate head of bacteriophage T4.
Authors: Andrei Fokine / Paul R Chipman / Petr G Leiman / Vadim V Mesyanzhinov / Venigalla B Rao / Michael G Rossmann /
Abstract: The head of bacteriophage T4 is a prolate icosahedron with one unique portal vertex to which the phage tail is attached. The three-dimensional structure of mature bacteriophage T4 head has been ...The head of bacteriophage T4 is a prolate icosahedron with one unique portal vertex to which the phage tail is attached. The three-dimensional structure of mature bacteriophage T4 head has been determined to 22-A resolution by using cryo-electron microscopy. The T4 capsid has a hexagonal surface lattice characterized by the triangulation numbers T(end) = 13 laevo for the icosahedral caps and T(mid) = 20 for the midsection. Hexamers of the major capsid protein gene product (gp)23* and pentamers of the vertex protein gp24*, as well as the outer surface proteins highly antigenic outer capsid protein (hoc) and small outer capsid protein (soc), are clearly evident in the reconstruction. The size and shape of the gp23* hexamers are similar to the major capsid protein organization of bacteriophage HK97. The binding sites and shape of the hoc and soc proteins have been established by analysis of the soc(-) and hoc(-)soc(-) T4 structures.
History
DepositionJul 20, 2007-
Header (metadata) releaseAug 28, 2007-
Map releaseAug 28, 2007-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1414.gif

Downloads & links

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Map

FileDownload / File: emd_1414.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the bacteriophage T4 prolate head using D5 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.96 Å/pix.
x 224 pix.
= 1335.04 Å		5.96 Å/pix.
x 224 pix.
= 1335.04 Å		5.96 Å/pix.
x 224 pix.
= 1335.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.96 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.27 / Movie #1: 1.5
Minimum - Maximum-3.80172 - 7.14993
Average (Standard dev.)-0.00000000617085 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 1335.04 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.965.965.96
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z1335.0401335.0401335.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-90
NX/NY/NZ181181181
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-3.8027.150-0.000

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Supplemental data

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Sample components

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Entire : Bacteriophage T4 capsid

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

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Supramolecule #1000: Bacteriophage T4 capsid

SupramoleculeName: Bacteriophage T4 capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: T4 capsid / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: T4 capsid
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gp23 / Diameter: 1200 Å / T number (triangulation number): 13
Virus shellShell ID: 2 / Name: gp23 / T number (triangulation number): 20

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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: 6.2
Details: Distilled water. The concentration of the virus particles was 10E11 particles per ml.
GridDetails: quantifoil copper grid 2um holes
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: in-house, gravity driven plunger
Method: 3.5ul of sample hand blotted approx. 1sec

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 97 K
Alignment procedureLegacy - Astigmatism: live fft at 190,000x
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 100 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, EMAN
Details: The reconstruction was calculated assuming D5 symmetry. FSC=0.5 at 21 A, FSC=0.3 at 17 A.
Number images used: 6390

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