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- EMDB-5233: CryoEM structure of cytoplasmic polyhedrosis virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5233
TitleCryoEM structure of cytoplasmic polyhedrosis virus
Map dataThis is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus
Sample
  • Sample: Cytoplasmic Polyhedrosis Virus
  • Virus: Cypovirus (cytoplasmic polyhedrosis viruses)
Keywordscryoelectron microscopy
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid
Similarity search - Function
: / Viral structural protein 5 / : / CPV Capsid shell protein VP1, small protrusion domain / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain ...: / Viral structural protein 5 / : / 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
Viral structural protein 5 / VP1 / Capsid protein VP1 / Structural protein VP3
Similarity search - Component
Biological speciesCypovirus (cytoplasmic polyhedrosis viruses)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCheng L / Sun J / Zhang K / Mou Z / Huang X / Ji G / Sun F / Zhang J / Zhu P
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.
Authors: Lingpeng Cheng / Jingchen Sun / Kai Zhang / Zongjun Mou / Xiaoxing Huang / Gang Ji / Fei Sun / Jingqiang Zhang / Ping Zhu /
Abstract: The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of "turreted" reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full ...The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of "turreted" reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full atomic model of CPV built from a 3D density map obtained using cryoelectron microscopy. The image data for the 3D reconstruction were acquired exclusively from a CCD camera. Our structure shows that the enzymatic domains of the pentameric turret of CPV are topologically conserved and that there are five unique channels connecting the guanylyltransferase and methyltransferase regions. This structural organization reveals how the channels guide nascent mRNA sequentially to guanylyltransferase, 7-N-methyltransferase, and 2'-O-methyltransferase in the turret, undergoing the highly coordinated mRNA capping activity. Furthermore, by fitting the deduced amino acid sequence of the protein VP5 to 120 large protrusion proteins on the CPV capsid shell, we confirmed that this protrusion protein is encoded by CPV RNA segment 7.
History
DepositionSep 14, 2010-
Header (metadata) releaseMar 10, 2011-
Map releaseMar 10, 2011-
UpdateApr 2, 2012-
Current statusApr 2, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iz3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5233_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5233.map.gz / Format: CCP4 / Size: 762.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 500 pix.
= 595. Å		1.19 Å/pix.
x 640 pix.
= 761.6 Å		1.19 Å/pix.
x 640 pix.
= 761.6 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: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-16.951129909999999 - 18.036975859999998
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-3200
Dimensions640640500
Spacing640640500
CellA: 761.60004 Å / B: 761.60004 Å / C: 595.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.191.191.19
M x/y/z640640500
origin x/y/z0.0000.0000.000
length x/y/z761.600761.600595.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-320-3200
NC/NR/NS640640500
D min/max/mean-16.95118.0370.000

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Supplemental data

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Sample components

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Entire : Cytoplasmic Polyhedrosis Virus

EntireName: Cytoplasmic Polyhedrosis Virus
Components
  • Sample: Cytoplasmic Polyhedrosis Virus
  • Virus: Cypovirus (cytoplasmic polyhedrosis viruses)

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Supramolecule #1000: Cytoplasmic Polyhedrosis Virus

SupramoleculeName: Cytoplasmic Polyhedrosis Virus / type: sample / ID: 1000 / Number unique components: 5

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Supramolecule #1: Cypovirus

SupramoleculeName: Cypovirus / type: virus / ID: 1 / Name.synonym: CPV / NCBI-ID: 10981 / Sci species name: Cypovirus / Database: NCBI / 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: 720 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: 7.5
GridDetails: 200 mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateApr 10, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 1.19 µm / Number real images: 1600 / Average electron dose: 20 e/Å2 / Bits/pixel: 24
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 75000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMIRS / Number images used: 29000

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