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

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Basic information

Entry
Database: EMDB / ID: EMD-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).
Sample
  • Sample: cytoplasmic polyhedrosis virus
  • Virus: Bombyx mori cypovirus 1
Keywordsvirus / strcuture / CPV / cryo-electron microscopy
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid
Similarity search - Function
: / CPV Capsid shell protein VP1, small protrusion domain / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 ...: / CPV Capsid shell protein VP1, small protrusion domain / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / : / Inner layer core protein VP1-like, C-terminal
Similarity search - Domain/homology
Inner capsid protein VP1 / VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
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 /
Abstract: Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell ...Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation. Here we report the three-dimensional structure of CPV at 3.88 A resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of alpha-helices, the strand separation in beta-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-beta-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications.
History
DepositionApr 15, 2008-
Header (metadata) releaseApr 16, 2008-
Map releaseMar 31, 2009-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: PDBe / Status: Released

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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 modelsPDB-3cnf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1508.gif

Downloads & links

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Map

FileDownload / File: emd_1508.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the whole cryoEM 2f map for the icosahedral Cytoplasmic Polyhedrosis Virus (CPV).
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.644 / Movie #1: 0.8
Minimum - Maximum0.0 - 8.028090000000001
Average (Standard dev.)0.0903673 (±0.386624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-385-385-385
Dimensions771771771
Spacing771771771
CellA=B=C: 747.87 Å
α=β=γ: 90 °

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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Segmentation: This is a segment of the asymmetric unit

AnnotationThis is a segment of the asymmetric unit
Fileemd_1508_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cytoplasmic polyhedrosis virus

EntireName: cytoplasmic polyhedrosis virus
Components
  • Sample: cytoplasmic polyhedrosis virus
  • Virus: Bombyx mori cypovirus 1

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Supramolecule #1000: cytoplasmic polyhedrosis virus

SupramoleculeName: cytoplasmic polyhedrosis virus / type: sample / ID: 1000 / Details: whole infectious virus / Oligomeric state: icosahedral particle of whole virus / Number unique components: 5

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Supramolecule #1: Bombyx mori cypovirus 1

SupramoleculeName: Bombyx mori cypovirus 1 / type: virus / ID: 1 / Name.synonym: CPV
Details: CPV is an unenveloped virus wiht a single-shell capsid and diameter of 750 Angstroms.
NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: CPV
Host (natural)Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 750 Å / T number (triangulation number): 1

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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: 7.4 / Details: 10mM PBS
GridDetails: the holes of holey carbon films
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER
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 ...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.
Method: blot for 3 seconds wiht filter paper before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 100 K
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: 154380 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 154380
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

DetailsFocal pairs of micrographs were recorded on 4KX4K charge-coupled device (CCD) camera.
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS
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 ...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.
Number images used: 12814

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