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- EMDB-5200: 5.4-Angstrom cryoEM structure of the Bordetella Bacteriophage capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5200
Title5.4-Angstrom cryoEM structure of the Bordetella Bacteriophage capsid
Map dataThis is the cryoEM density map for half of the icosahedral capsid of a bacterial phage, BPP.
Sample
  • Sample: Bordetella Bacteriophage
  • Virus: Bordetella Bacteriophage
KeywordsBordetella Bacteriophage / capsid / cryoEM / structure / major capsid protein / cementing protein
Biological speciesBordetella Bacteriophage
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsJin L / Hodes A / Hui WH / Zhang X / Yu X / Miller JF / Zhou ZH
CitationJournal: To Be Published
Title: 5.4-Angstrom cryoEM structure of the Bordetella Bacteriophage capsid
Authors: Jin L / Hodes A / Hui WH / Zhang X / Zhang X / Yu X / Miller JF / Zhou ZH
History
DepositionMay 13, 2010-
Header (metadata) releaseMay 21, 2010-
Map releaseJul 18, 2011-
UpdateAug 2, 2011-
Current statusAug 2, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5200_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5200.map.gz / Format: CCP4 / Size: 763 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the cryoEM density map for half of the icosahedral capsid of a bacterial phage, BPP.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 372 pix.
= 361.435 Å		0.97 Å/pix.
x 742 pix.
= 720.927 Å		0.97 Å/pix.
x 742 pix.
= 720.927 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.9716 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 40.0 / Movie #1: 30
Minimum - Maximum-135.647999999999996 - 180.231999999999999
Average (Standard dev.)2.82442 (±22.841200000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-371-3710
Dimensions742742372
Spacing742742372
CellA: 720.927 Å / B: 720.927 Å / C: 361.435 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.971599730458220.971599730458220.97159946236559
M x/y/z742742372
origin x/y/z0.0000.0000.000
length x/y/z720.927720.927361.435
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-371-3710
NC/NR/NS742742372
D min/max/mean-135.648180.2322.824

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Supplemental data

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Sample components

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Entire : Bordetella Bacteriophage

EntireName: Bordetella Bacteriophage
Components
  • Sample: Bordetella Bacteriophage
  • Virus: Bordetella Bacteriophage

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Supramolecule #1000: Bordetella Bacteriophage

SupramoleculeName: Bordetella Bacteriophage / type: sample / ID: 1000
Details: The whole phage (with portal and tail structures) were imaged initially. After icosahedral averaging in 3D reconstruction, the resulting density map covers only the capsid.
Oligomeric state: Icosahedral particle made of the major capsid protein and the cementing protein
Number unique components: 2

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Supramolecule #1: Bordetella Bacteriophage

SupramoleculeName: Bordetella Bacteriophage / type: virus / ID: 1 / Name.synonym: Bordetella phage / Sci species name: Bordetella Bacteriophage / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Bordetella phage
Host (natural)Organism: Bordetella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 685 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

BufferpH: 7.5 / Details: 50mM Tris-HCl, 250mM NaCl
GridDetails: holey carbon films (Quantifoil, Germany) supported on 400-mesh copper grids
VitrificationCryogen name: NITROGEN / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: manual plunger. Vitrification was carried out using a house-made manual plunger.
Method: Blot for 2-3 seconds before plunging into liquid ethane

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K / Max: 105 K / Average: 100 K
DateOct 20, 2006
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 97940 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.72 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 97940
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe partilces were imaged with a 4kx4k TVIPS CCD camera.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS / Details: Focal pair method / Number images used: 18524

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