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- EMDB-1164: Maturation of phage T7 involves structural modification of both s... -

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Basic information

Entry
Database: EMDB / ID: EMD-1164
TitleMaturation of phage T7 involves structural modification of both shell and inner core components.
Map databacteriophage T7 mature virion
Sample
  • Sample: phage T7 mature virion
  • Protein or peptide: gp14
  • Protein or peptide: gp15
  • Protein or peptide: gp16
  • Protein or peptide: gp8
  • Protein or peptide: gp10A
  • Protein or peptide: gp10B
  • Protein or peptide: gp11
  • Protein or peptide: gp12
  • Protein or peptide: gp17
  • DNA: genome
Biological speciesEnterobacteria phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsAgirrezabala X / Martin-Benito J / Caston JR / Miranda R / Valpuesta JM / Carrascosa JL
CitationJournal: EMBO J / Year: 2005
Title: Maturation of phage T7 involves structural modification of both shell and inner core components.
Authors: Xabier Agirrezabala / Jaime Martín-Benito / José R Castón / Roberto Miranda / José María Valpuesta / José L Carrascosa /
Abstract: The double-stranded DNA bacteriophages are good model systems to understand basic biological processes such as the macromolecular interactions that take place during the virus assembly and ...The double-stranded DNA bacteriophages are good model systems to understand basic biological processes such as the macromolecular interactions that take place during the virus assembly and maturation, or the behavior of molecular motors that function during the DNA packaging process. Using cryoelectron microscopy and single-particle methodology, we have determined the structures of two phage T7 assemblies produced during its morphogenetic process, the DNA-free prohead and the mature virion. The first structure reveals a complex assembly in the interior of the capsid, which involves the scaffolding, and the core complex, which plays an important role in DNA packaging and is located in one of the phage vertices. The reconstruction of the mature virion reveals important changes in the shell, now much larger and thinner, the disappearance of the scaffolding structure, and important rearrangements of the core complex, which now protrudes the shell and interacts with the tail. Some of these changes must originate by the pressure exerted by the DNA in the interior of the head.
History
DepositionSep 22, 2005-
Header (metadata) releaseSep 22, 2005-
Map releaseSep 22, 2006-
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: 0.19
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.19
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1164.gif

Downloads & links

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Map

FileDownload / File: emd_1164.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbacteriophage T7 mature virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.66 Å/pix.
x 220 pix.
= 1025.2 Å		4.66 Å/pix.
x 220 pix.
= 1025.2 Å		4.66 Å/pix.
x 220 pix.
= 1025.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.66 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.187 / Movie #1: 0.19
Minimum - Maximum-0.69639 - 0.836632
Average (Standard dev.)-0.00658687 (±0.104622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 1025.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.664.664.66
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z1025.2001025.2001025.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.6960.837-0.007

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Supplemental data

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Sample components

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Entire : phage T7 mature virion

EntireName: phage T7 mature virion
Components
  • Sample: phage T7 mature virion
  • Protein or peptide: gp14
  • Protein or peptide: gp15
  • Protein or peptide: gp16
  • Protein or peptide: gp8
  • Protein or peptide: gp10A
  • Protein or peptide: gp10B
  • Protein or peptide: gp11
  • Protein or peptide: gp12
  • Protein or peptide: gp17
  • DNA: genome

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Supramolecule #1000: phage T7 mature virion

SupramoleculeName: phage T7 mature virion / type: sample / ID: 1000 / Number unique components: 10

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Macromolecule #1: gp14

MacromoleculeName: gp14 / type: protein_or_peptide / ID: 1 / Details: core protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 20.8 MDa

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Macromolecule #2: gp15

MacromoleculeName: gp15 / type: protein_or_peptide / ID: 2 / Details: core protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 84.2 MDa

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Macromolecule #3: gp16

MacromoleculeName: gp16 / type: protein_or_peptide / ID: 3 / Details: core protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 143.8 MDa

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Macromolecule #4: gp8

MacromoleculeName: gp8 / type: protein_or_peptide / ID: 4 / Details: connector / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 58.9 MDa

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Macromolecule #5: gp10A

MacromoleculeName: gp10A / type: protein_or_peptide / ID: 5 / Details: head protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 36.9 MDa

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Macromolecule #6: gp10B

MacromoleculeName: gp10B / type: protein_or_peptide / ID: 6 / Details: head protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 45.4 MDa

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Macromolecule #7: gp11

MacromoleculeName: gp11 / type: protein_or_peptide / ID: 7 / Details: tail protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 22.2 MDa

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Macromolecule #8: gp12

MacromoleculeName: gp12 / type: protein_or_peptide / ID: 8 / Details: tail protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 89.26 MDa

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Macromolecule #9: gp17

MacromoleculeName: gp17 / type: protein_or_peptide / ID: 9 / Details: tail protein / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage
Molecular weightTheoretical: 61.4 MDa

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Macromolecule #10: genome

MacromoleculeName: genome / type: dna / ID: 10 / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Enterobacteria phage T7 (virus) / synonym: T7 phage

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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 F20
Alignment procedureLegacy - Astigmatism: FFT with ssCCD
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Average electron dose: 10 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 29930 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. GATAN. Eucentric
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Wiener filter, defocus groups
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: 5-fold symmetrya / Number images used: 4785

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