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- EMDB-5445: Icosahedral reconstruction of the Streptococcus phage C1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5445
TitleIcosahedral reconstruction of the Streptococcus phage C1 capsid
Map dataicosahedral reconstruction of phage C1 capsid
Sample
  • Sample: C1 capsid
  • Virus: Streptococcus phage C1 (virus)
Keywordsbacteriophage / capsid / HK97 fold / Podoviridae
Biological speciesStreptococcus phage C1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsAksyuk AA / Bowman VD / Kaufmann B / Fields C / Klose T / Holdaway HA / Fischetti VA / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry.
Authors: Anastasia A Aksyuk / Valorie D Bowman / Bärbel Kaufmann / Christopher Fields / Thomas Klose / Heather A Holdaway / Vincent A Fischetti / Michael G Rossmann /
Abstract: The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus ...The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus were calculated using cryo-electron microscopy. The capsid protein has an HK97 fold arranged into a T = 4 icosahedral lattice. The C1 tail is terminated with a ϕ29-like knob, surrounded by a skirt of twelve long appendages with novel morphology. Several C1 structural proteins have been identified, including a candidate for an appendage. The crystal structure of the knob has an N-terminal domain with a fold observed previously in tube forming proteins of Siphoviridae and Myoviridae phages. The structure of C1 suggests the mechanisms by which the virus digests the cell wall and ejects its genome. Although there is little sequence similarity to other phages, conservation of the structural proteins demonstrates a common origin of the head and tail, but more recent evolution of the appendages.
History
DepositionJul 10, 2012-
Header (metadata) releaseAug 1, 2012-
Map releaseAug 22, 2012-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • 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_5445.map.gz / Format: CCP4 / Size: 586.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedral reconstruction of phage C1 capsid
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-5.16426134 - 7.88251734
Average (Standard dev.)0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 567.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z567.000567.000567.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS540540540
D min/max/mean-5.1647.8830.000

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Supplemental data

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Sample components

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Entire : C1 capsid

EntireName: C1 capsid
Components
  • Sample: C1 capsid
  • Virus: Streptococcus phage C1 (virus)

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Supramolecule #1000: C1 capsid

SupramoleculeName: C1 capsid / type: sample / ID: 1000 / Oligomeric state: T=4 capsid / Number unique components: 1

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Supramolecule #1: Streptococcus phage C1

SupramoleculeName: Streptococcus phage C1 / type: virus / ID: 1 / NCBI-ID: 230871 / Sci species name: Streptococcus phage C1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Streptococcus (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: C1 / Diameter: 500 Å / T number (triangulation number): 4

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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

VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateMay 1, 2011
Image recordingDigitization - Scanner: NIKON COOLSCAN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 17000

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