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- EMDB-5730: Asymmetric reconstruction of phage Sf6 -

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Basic information

Entry
Database: EMDB / ID: EMD-5730
TitleAsymmetric reconstruction of phage Sf6
Map dataasymmetric reconstruction of phage Sf6
Sample
  • Sample: phage sf6 mature virion
  • Virus: Shigella phage Sf6 (virus)
Biological speciesShigella phage Sf6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsParent KN / Gilcrease EB / Casjens SR / Baker TS
CitationJournal: Virology / Year: 2012
Title: Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures.
Authors: Kristin N Parent / Eddie B Gilcrease / Sherwood R Casjens / Timothy S Baker /
Abstract: Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig- ...Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.
History
DepositionJul 26, 2013-
Header (metadata) releaseAug 7, 2013-
Map releaseAug 7, 2013-
UpdateAug 28, 2013-
Current statusAug 28, 2013Processing site: RCSB / 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
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  • 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

Downloads & links

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Map

FileDownload / File: emd_5730.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationasymmetric reconstruction of phage Sf6
Voxel sizeX=Y=Z: 2.14 Å
Density
Contour LevelBy AUTHOR: 1.7 / Movie #1: 1.5
Minimum - Maximum-9.47240639 - 18.035875319999999
Average (Standard dev.)0.08315878 (±2.12381506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-350-350-350
Dimensions701701701
Spacing701701701
CellA=B=C: 1500.14 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.142.142.14
M x/y/z701701701
origin x/y/z0.0000.0000.000
length x/y/z1500.1401500.1401500.140
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-350-350-350
NC/NR/NS701701701
D min/max/mean-9.47218.0360.083

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Supplemental data

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Sample components

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Entire : phage sf6 mature virion

EntireName: phage sf6 mature virion
Components
  • Sample: phage sf6 mature virion
  • Virus: Shigella phage Sf6 (virus)

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Supramolecule #1000: phage sf6 mature virion

SupramoleculeName: phage sf6 mature virion / type: sample / ID: 1000
Oligomeric state: icosahedral head, trimeric tail needle, 6-fold tailspikes, 12-fold portal and gp4
Number unique components: 14

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Supramolecule #1: Shigella phage Sf6

SupramoleculeName: Shigella phage Sf6 / type: virus / ID: 1 / NCBI-ID: 10761 / Sci species name: Shigella phage Sf6 / Sci species strain: clear mutant / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri (bacteria) / Strain: PE577 / synonym: BACTERIA(EUBACTERIA)

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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

Concentration10 mg/mL
BufferpH: 7.6 / Details: 10mM Tris, 10mM MgCl2
GridDetails: 400 mesh Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 5 sec before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: 4.61 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER
TemperatureMin: 89 K / Max: 91 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at high magnification
DateSep 30, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.07 µm / Number real images: 611 / Average electron dose: 22 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Robem
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 16253
Detailsthe reconstruction was done using Auto3dem.

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