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- EMDB-5388: Cryo-electron microscopy and three-dimensional reconstruction of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5388
TitleCryo-electron microscopy and three-dimensional reconstruction of bacteriophage CW02
Map dataEMD-5388
Sample
  • Sample: Bacteriophage CW02
  • Virus: Bacteriophage CW02 (virus)
Keywordshalophage / bacteriophage / bacteriophage HK97 / bacteriophage T7 / T7-like phage / turret / extremophile / Great Salt Lake
Function / homologyPhage capsid / Phage capsid family / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesBacteriophage CW02 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsShen PS / Domek MJ / Sanz-Garcia E / Makaju A / Taylor R / Culumber M / Breakwell DP / Prince JT / Belnap DM
CitationJournal: J Virol / Year: 2012
Title: Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.
Authors: Peter S Shen / Matthew J Domek / Eduardo Sanz-García / Aman Makaju / Ryan M Taylor / Ryan Hoggan / Michele D Culumber / Craig J Oberg / Donald P Breakwell / John T Prince / David M Belnap /
Abstract: Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, ...Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.
History
DepositionJan 31, 2012-
Header (metadata) releaseFeb 7, 2012-
Map releaseMay 21, 2012-
UpdateMay 21, 2012-
Current statusMay 21, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 52.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 52.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j1a
  • Surface level: 52.8
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j1a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5388_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5388.map.gz / Format: CCP4 / Size: 68.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMD-5388
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.14 Å/pix.
x 264 pix.
= 860.36 Å		3.14 Å/pix.
x 264 pix.
= 860.36 Å		3.14 Å/pix.
x 264 pix.
= 860.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 52.799999999999997 / Movie #1: 52.8
Minimum - Maximum-200.557861330000009 - 265.767730710000023
Average (Standard dev.)11.445621490000001 (±41.381351469999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-131-131-131
Dimensions264264264
Spacing274274274
CellA=B=C: 860.36005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.143.143.14
M x/y/z274274274
origin x/y/z0.0000.0000.000
length x/y/z860.360860.360860.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-131-131-131
NC/NR/NS264264264
D min/max/mean-200.558265.76811.446

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Supplemental data

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Sample components

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Entire : Bacteriophage CW02

EntireName: Bacteriophage CW02 (virus)
Components
  • Sample: Bacteriophage CW02
  • Virus: Bacteriophage CW02 (virus)

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Supramolecule #1000: Bacteriophage CW02

SupramoleculeName: Bacteriophage CW02 / type: sample / ID: 1000 / Details: Sample buffer solution contains 8% NaCl / Oligomeric state: head and tail phage / Number unique components: 1

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Supramolecule #1: Bacteriophage CW02

SupramoleculeName: Bacteriophage CW02 / type: virus / ID: 1 / Sci species name: Bacteriophage CW02 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salinivibrio costicola (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gp48 / Diameter: 691 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

Concentration3 mg/mL
BufferpH: 8
Details: 1.35 M NaCl, 48 mM MgSO4-7H2O, 1 mM CaCl2, 2 mM Tris-Cl
GridDetails: 200 mesh, holey-carbon-coated copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 92 K / Max: 94 K / Average: 93 K
DateJul 1, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 1.57 µm / Number real images: 8695
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37564 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsParticles were manually selected using X3D
CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT2,EM3DR2,(PFT3DR) / Number images used: 8695
Final angle assignmentDetails: PFT2

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Atomic model buiding 1

Initial modelPDB ID:

1ohg


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G
SoftwareName: Chimera
DetailsProtocol: Automatic rigid body. C-alpha coordinates pertaining to the HK97-fold were separately fitted as rigid bodies into capsid hexamers or pentamers.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j1a:
HK97-like fold fitted into 3D reconstruction of bacteriophage CW02

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