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- EMDB-1075: Molecular architecture of the prolate head of bacteriophage T4. -

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Basic information

Entry
Database: EMDB / ID: EMD-1075
TitleMolecular architecture of the prolate head of bacteriophage T4.
Map datacryoEM reconstruction of the bacteriophage T4 head
Sample
  • Sample: bacteriophage T4 prolate head
  • Virus: Enterobacteria phage T4 (virus)
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.5 Å
AuthorsFokine A / Chipman PR / Leiman PG / Mesyanzhinov VV / Rao VB / Rossmann MG
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
DepositionMar 23, 2004-
Header (metadata) releaseMar 29, 2004-
Map releaseMar 29, 2004-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1075.gif

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400_10752.gif

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400_10754.gif

400_10755.gif

400_10756.gif

400_10757.gif

400_10758.gif

400_10759.gif

emd_1075.tif

Downloads & links

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Map

FileDownload / File: emd_1075.map.gz / Format: CCP4 / Size: 27.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM reconstruction of the bacteriophage T4 head
Voxel sizeX=Y=Z: 5.96 Å
Density
Contour Level1: 0.0864 / Movie #1: 0.03
Minimum - Maximum-0.157651 - 0.263553
Average (Standard dev.)0.0133426 (±0.0458542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions175175240
Spacing175175240
CellA: 1043 Å / B: 1043 Å / C: 1430.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.965.965.96
M x/y/z175175240
origin x/y/z0.0000.0000.000
length x/y/z1043.0001043.0001430.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS175175240
D min/max/mean-0.1580.2640.013

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Supplemental data

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Sample components

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Entire : bacteriophage T4 prolate head

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

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Supramolecule #1000: bacteriophage T4 prolate head

SupramoleculeName: bacteriophage T4 prolate head / type: sample / ID: 1000
Details: Sample was the native bacteriophage T4. Only the head part of the phage was reconstructed.
Number unique components: 1
Molecular weightExperimental: 194 MDa / Method: STEM, 194 MDa is the mass of the DNA filled head.

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: phage T4 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: phage T4
Host (natural)Organism: Ecoli / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 194 MDa
Virus shellShell ID: 1 / Name: capsid width is 860 A, length is 1195 A
Virus shellShell ID: 2 / Name: Tmid=20; Tend=13

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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 pre 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
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: 55 / Average electron dose: 29 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: The reconstruction was made in SPIDER using the projection matching protocol. The reference projections were calculated in the interval theta: 0-90 degrees, phi: 0-72 degrees.
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.5 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: SPIDER
Details: The reconstruction was performed by imposing 5-fold symmetry averaging. The 5-fold axis is along Z.
Number images used: 5140

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Atomic model buiding 1

DetailsNothing to fit

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