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- EMDB-1810: Phage T7 empty head. -

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Basic information

Entry
Database: EMDB / ID: EMD-1810
TitlePhage T7 empty head.
Map dataBacteriophage T7 empty head
Sample
  • Sample: Phage T7 empty head
  • Virus: Enterobacteria phage T7 (virus)
KeywordsBacteriophage / virus / capsid maturation / cryoelectron microscopy / morphogenetic intermediate.
Function / homologyCapsid Gp10A/Gp10B / : / Major capsid protein / viral capsid / viral translational frameshifting / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsIonel A / Velazquez-Muriel JA / Luque D / Cuervo A / Caston JR / Valpuesta JM / Martin-Benito J / Carrascosa JL
CitationJournal: J Biol Chem / Year: 2011
Title: Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
Authors: Alina Ionel / Javier A Velázquez-Muriel / Daniel Luque / Ana Cuervo / José R Castón / José M Valpuesta / Jaime Martín-Benito / José L Carrascosa /
Abstract: Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for ...Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for infecting a host under challenging environmental conditions. Here, we determine the mature capsid structure of T7 at 1 nm resolution by cryo-electron microscopy and compare it with the prohead to reveal the molecular basis of T7 shell maturation. The mature capsid presents an expanded and thinner shell, with a drastic rearrangement of the major protein monomers that increases in their interacting surfaces, in turn resulting in a new bonding lattice. The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A- and P-domains of each subunit. The unique features of this shell transformation, which does not employ the accessory proteins, inserted domains, or molecular interactions observed in other phages, suggest a simple capsid assembling strategy that may have appeared early in the evolution of these viruses.
History
DepositionOct 24, 2010-
Header (metadata) releaseNov 5, 2010-
Map releaseNov 5, 2010-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xvr
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xvr
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xvr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1810_T7matur...

Downloads & links

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Map

FileDownload / File: emd_1810.map.gz / Format: CCP4 / Size: 626.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage T7 empty head
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 552 pix.
= 772.8 Å		1.4 Å/pix.
x 552 pix.
= 772.8 Å		1.4 Å/pix.
x 552 pix.
= 772.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.00872735 - 0.0178209
Average (Standard dev.)0.0000675162 (±0.0022955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions552552552
Spacing552552552
CellA=B=C: 772.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z552552552
origin x/y/z0.0000.0000.000
length x/y/z772.800772.800772.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-69-69-68
NX/NY/NZ138138138
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS552552552
D min/max/mean-0.0090.0180.000

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Supplemental data

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Sample components

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Entire : Phage T7 empty head

EntireName: Phage T7 empty head
Components
  • Sample: Phage T7 empty head
  • Virus: Enterobacteria phage T7 (virus)

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Supramolecule #1000: Phage T7 empty head

SupramoleculeName: Phage T7 empty head / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1

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Supramolecule #1: Enterobacteria phage T7

SupramoleculeName: Enterobacteria phage T7 / type: virus / ID: 1 / Name.synonym: Bacteriophage T7 / NCBI-ID: 10760 / Sci species name: Enterobacteria phage T7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Bacteriophage T7
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 600 Å / T number (triangulation number): 7

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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: 7.8 / Details: 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 0.1 M NaCl
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: xmipp / Number images used: 5100

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Atomic model buiding 1

Initial modelPDB ID:

1ohg

SoftwareName: Xmipp
RefinementSpace: REAL
Output model

PDB-2xvr:
Phage T7 empty mature head shell

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