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- EMDB-1508: 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by sing... -

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Entry
Database: EMDB / ID: 1508
Title3.88 Angstrom structure of cytoplasmic polyhedrosis virus by single-particle cryo-electron microscopy
Map dataThis is the whole cryoEM 2f map for the icosahedral Cytoplasmic Polyhedrosis Virus (CPV).
Samplecytoplasmic polyhedrosis virus:
virus
Keywordsvirus / strcuture / CPV / cryo-electron microscopy
Function / homologyT=2 icosahedral viral capsid / viral inner capsid / Capsid protein VP1 / VP3
Function and homology information
SourceBombyx mori cypovirus 1 (CPV)
Methodsingle particle reconstruction / cryo EM / 3.88 Å resolution
AuthorsYU X / Jin L / Zhou ZH
CitationJournal: Nature / Year: 2008
Title: 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
Authors: Xuekui Yu / Lei Jin / Z Hong Zhou
Validation ReportPDB-ID: 3cnf

SummaryFull reportAbout validation report
DateDeposition: Apr 15, 2008 / Header (metadata) release: Apr 16, 2008 / Map release: Mar 31, 2009 / Last update: Dec 26, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3cnf
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3cnf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1508.map.gz (map file in CCP4 format, 1790291 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
771 pix
0.97 Å/pix.
= 747.87 Å
771 pix
0.97 Å/pix.
= 747.87 Å
771 pix
0.97 Å/pix.
= 747.87 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density
Contour Level:0.644 (by author), 0.8 (movie #1):
Minimum - Maximum0 - 8.02809
Average (Standard dev.)0.0903673 (0.386624)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions771771771
Origin-385-385-385
Limit385385385
Spacing771771771
CellA=B=C: 747.87 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.970.970.97
M x/y/z771771771
origin x/y/z0.0000.0000.000
length x/y/z747.870747.870747.870
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-385-385-385
NC/NR/NS771771771
D min/max/mean0.0008.0280.090

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Supplemental data

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Mask #1

Fileemd_1508_msk.map ( map file in CCP4 format, 15279 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::EMD-1508::::MASK:1::::
Annotation detailsThis is a segment of the asymmetric unit

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Sample components

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Entire cytoplasmic polyhedrosis virus

EntireName: cytoplasmic polyhedrosis virus / Details: whole infectious virus / Number of components: 5 / Oligomeric State: icosahedral particle of whole virus

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Component #1: virus, Bombyx mori cypovirus 1

VirusName: Bombyx mori cypovirus 1 / a.k.a: CPV / Class: VIRION
Details: CPV is an unenveloped virus wiht a single-shell capsid and diameter of 750 Angstroms.
Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Bombyx mori cypovirus 1 (CPV)
Source (natural)Host Species: Bombyx mori (domestic silkworm) / Host category: INVERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 10mM PBS / pH: 7.4
Support filmthe holes of holey carbon films
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K
Method: blot for 3 seconds wiht filter paper before plunging
Details: Vitrification instrument: lab-made plunger. Vitrification was carried out at room temperature. CPV were embedded in a thin layer of vitreous ice suspended across the holes of holey carbon films for cryoEM imaging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 154380 X (nominal), 154380 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 150 - 1300 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: GENERIC TVIPS

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Image processing

ProcessingMethod: single particle reconstruction
Details: Focal pairs of micrographs were recorded on 4KX4K charge-coupled device (CCD) camera.
Number of projections: 12814 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier common lines and Fourier-Bessel synthesis
Software: IMIRS / CTF correction: each particle
Details: Determination of particle orientation and center parameters and subsequent 3D reconstruction were carried out using programs in the IMIRS software package, which are based on Fourier common lines and Fourier-Bessel synthesis methods. Prior to the merging of particles for 3D reconstruction, the Fourier transform values of individual images were corrected for the CTF with 15 percent amplitude contrast and a decay factor of 35 sq. Angstroms.
Resolution: 3.88 Å / Resolution method: FSC 0.5

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