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- EMDB-1321: Quasi-atomic model of bacteriophage t7 procapsid shell: insights ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1321
TitleQuasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Map dataphage T7 prohead icosahedral map
Sample
  • Sample: phage T7 prohead
  • Protein or peptide: gp10A
Function / homologyCapsid Gp10A/Gp10B / : / Major capsid protein / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsAgirrezabala X / Velazquez-Muriel J / Gomez-Puertas P / Scheres S / Carazo JM / Carrascosa JL
CitationJournal: Structure / Year: 2007
Title: Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Authors: Xabier Agirrezabala / Javier A Velázquez-Muriel / Paulino Gómez-Puertas / Sjors H W Scheres / José M Carazo / José L Carrascosa /
Abstract: The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. ...The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. Tailed bacteriophages are emerging as one such family, and we have studied the possible existence of the HK97-like fold in bacteriophage T7. The procapsid structure at approximately 10 A resolution was used to obtain a quasi-atomic model by fitting a homology model of the T7 capsid protein gp10 that was based on the atomic structure of the HK97 capsid protein. A number of fold similarities, such as the fitting of domains A and P into the L-shaped procapsid subunit, are evident between both viral systems. A different feature is related to the presence of the amino-terminal domain of gp10 found at the inner surface of the capsid that might play an important role in the interaction of capsid and scaffolding proteins.
History
DepositionFeb 7, 2007-
Header (metadata) releaseFeb 7, 2007-
Map releaseJun 12, 2007-
UpdateAug 31, 2011-
Current statusAug 31, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 110
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 110
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3izg
  • Surface level: 110
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3izg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1321.gif

Downloads & links

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Map

FileDownload / File: emd_1321.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphage T7 prohead icosahedral map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 260 pix.
= 707.2 Å		2.72 Å/pix.
x 260 pix.
= 707.2 Å		2.72 Å/pix.
x 260 pix.
= 707.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 98.0 / Movie #1: 110
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)30.1645 (±48.0274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-130-130-130
Dimensions260260260
Spacing260260260
CellA=B=C: 707.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.722.722.72
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z707.200707.200707.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-130-130-130
NC/NR/NS260260260
D min/max/mean0.000255.00030.165

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Supplemental data

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Sample components

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Entire : phage T7 prohead

EntireName: phage T7 prohead
Components
  • Sample: phage T7 prohead
  • Protein or peptide: gp10A

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Supramolecule #1000: phage T7 prohead

SupramoleculeName: phage T7 prohead / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: gp10A

MacromoleculeName: gp10A / type: protein_or_peptide / ID: 1 / Name.synonym: major capsid protein / Number of copies: 420 / Oligomeric state: icosahedral / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: phage T7
Molecular weightTheoretical: 37 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 7.7 / Details: 50mM Tris-HCl pH:7.7 10mM MgCl2 100mM NaCl
GridDetails: Quantifoil grids 2/2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51600 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. GATAN. Eucentric
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: 100k
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Wiener filter, defocus groups
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 4460

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