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- EMDB-1580: CryoEM and 3D image reconstruction of Chilo Iridescent virus at 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-1580
TitleCryoEM and 3D image reconstruction of Chilo Iridescent virus at 13 angstrom resolution
Map dataChilo Iridescent virus at 13 angstrom resolution
Sample
  • Sample: CIV
  • Virus: Invertebrate iridescent virus 6
Keywordslarge DNA virus / cryo-electron microscopy / 3D image reconstruction / enveloped virus / minor capsid proteins
Biological speciesInvertebrate iridescent virus 6
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsYan X / Yu Z / Zhang P / Battisti AJ / Holdaway HA / Chipman PR / Bajaj C / Bergoin M / Rossmann MG / Baker TS
CitationJournal: J Mol Biol / Year: 2009
Title: The capsid proteins of a large, icosahedral dsDNA virus.
Authors: Xiaodong Yan / Zeyun Yu / Ping Zhang / Anthony J Battisti / Heather A Holdaway / Paul R Chipman / Chandrajit Bajaj / Max Bergoin / Michael G Rossmann / Timothy S Baker /
Abstract: Chilo iridescent virus (CIV) is a large (approximately 1850 A diameter) insect virus with an icosahedral, T=147 capsid, a double-stranded DNA (dsDNA) genome, and an internal lipid membrane. The ...Chilo iridescent virus (CIV) is a large (approximately 1850 A diameter) insect virus with an icosahedral, T=147 capsid, a double-stranded DNA (dsDNA) genome, and an internal lipid membrane. The structure of CIV was determined to 13 A resolution by means of cryoelectron microscopy (cryoEM) and three-dimensional image reconstruction. A homology model of P50, the CIV major capsid protein (MCP), was built based on its amino acid sequence and the structure of the homologous Paramecium bursaria chlorella virus 1 Vp54 MCP. This model was fitted into the cryoEM density for each of the 25 trimeric CIV capsomers per icosahedral asymmetric unit. A difference map, in which the fitted CIV MCP capsomers were subtracted from the CIV cryoEM reconstruction, showed that there are at least three different types of minor capsid proteins associated with the capsomers outside the lipid membrane. "Finger" proteins are situated at many, but not all, of the spaces between three adjacent capsomers within each trisymmetron, and "zip" proteins are situated between sets of three adjacent capsomers at the boundary between neighboring trisymmetrons and pentasymmetrons. Based on the results of segmentation and density correlations, there are at least eight finger proteins and three dimeric and two monomeric zip proteins in one asymmetric unit of the CIV capsid. These minor proteins appear to stabilize the virus by acting as intercapsomer cross-links. One transmembrane "anchor" protein per icosahedral asymmetric unit, which extends from beneath one of the capsomers in the pentasymmetron to the internal leaflet of the lipid membrane, may provide additional stabilization for the capsid. These results are consistent with the observations for other large, icosahedral dsDNA viruses that also utilize minor capsid proteins for stabilization and for determining their assembly.
History
DepositionNov 4, 2008-
Header (metadata) releaseNov 5, 2008-
Map releaseApr 1, 2009-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1580.gif

Downloads & links

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Map

FileDownload / File: emd_1580.map.gz / Format: CCP4 / Size: 389.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChilo Iridescent virus at 13 angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 471 pix.
= 1997.04 Å		4.24 Å/pix.
x 471 pix.
= 1997.04 Å		4.24 Å/pix.
x 471 pix.
= 1997.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.01 / Movie #1: 4
Minimum - Maximum-10.8142 - 23.1188
Average (Standard dev.)1.86893 (±3.8831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions471471471
Spacing471471471
CellA=B=C: 1997.04 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z471471471
origin x/y/z0.0000.0000.000
length x/y/z1997.0401997.0401997.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS471471471
D min/max/mean-10.81423.1191.869

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Supplemental data

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Sample components

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Entire : CIV

EntireName: CIV
Components
  • Sample: CIV
  • Virus: Invertebrate iridescent virus 6

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Supramolecule #1000: CIV

SupramoleculeName: CIV / type: sample / ID: 1000 / Details: CIV virions / Number unique components: 1

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Supramolecule #1: Invertebrate iridescent virus 6

SupramoleculeName: Invertebrate iridescent virus 6 / type: virus / ID: 1 / Name.synonym: chilo iridescent virus / NCBI-ID: 176652 / Sci species name: Invertebrate iridescent virus 6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: chilo iridescent virus
Host (natural)Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 1850 Å

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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

GridDetails: holey carbon film
VitrificationCryogen name: NITROGEN / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 210 / Average electron dose: 22 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 33000
Sample stageSpecimen holder: gatan 626 cryo holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 1800
Final two d classificationNumber classes: 1

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