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- EMDB-5256: 3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5256
Title3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus
Map dataThis is a cryoEM density map of cytoplasmic polyhedrosis virus
Sample
  • Sample: cytoplasmic polyhedrosis virus (CPV)
  • Virus: Bombyx mori cypovirus 1
Keywordscytoplasmic polyhedrosis virus / 3D reconstruction / cryoEM / full atom model
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid
Similarity search - Function
: / Viral structural protein 5 / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 ...: / Viral structural protein 5 / : / : / : / : / 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 / Inner layer core protein VP1-like, C-terminal
Similarity search - Domain/homology
Viral structural protein 5 / Capsid protein VP1 / Structural protein VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.1 Å
AuthorsYu X / Ge P / Jiang J / Atanasov I / Zhou ZH
CitationJournal: Structure / Year: 2011
Title: Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses.
Authors: Xuekui Yu / Peng Ge / Jiansen Jiang / Ivo Atanasov / Z Hong Zhou /
Abstract: Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we ...Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we report a 3.1 Å resolution cryo electron microscopy structure of CPV and derive its atomic model, consisting of 60 turret proteins (TPs), 120 each of capsid shell proteins (CSPs) and large protrusion proteins (LPPs). Two unique segments of CSP contribute to CPV's stability: an inserted protrusion domain interacting with neighboring proteins, and an N-anchor tying up CSPs together through strong interactions such as β sheet augmentation. Without the need to interact with outer shell proteins, LPP retains only the N-terminal two-third region containing a conserved helix-barrel core and interacts exclusively with CSP. TP is also simplified, containing only domains involved in RNA capping. Our results illustrate how CPV proteins have evolved in a coordinative manner to economically carry out their conserved functions.
History
DepositionJan 14, 2011-
Header (metadata) releaseJan 27, 2011-
Map releaseJun 23, 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: 16
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3izx
  • Surface level: 16
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3izx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5256_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5256.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryoEM density map of cytoplasmic polyhedrosis virus
Voxel sizeX=Y=Z: 1.104 Å
Density
Contour LevelBy AUTHOR: 16.0 / Movie #1: 16
Minimum - Maximum-47.52290344 - 87.34751129
Average (Standard dev.)0.80048662 (±5.88541937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-330-330-330
Dimensions660660660
Spacing660660660
CellA=B=C: 728.63995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1041.1041.104
M x/y/z660660660
origin x/y/z0.0000.0000.000
length x/y/z728.640728.640728.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-330-330-330
NC/NR/NS660660660
D min/max/mean-47.52387.3480.800

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Supplemental data

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Sample components

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Entire : cytoplasmic polyhedrosis virus (CPV)

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

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Supramolecule #1000: cytoplasmic polyhedrosis virus (CPV)

SupramoleculeName: cytoplasmic polyhedrosis virus (CPV) / type: sample / ID: 1000 / Details: CPV particles were purified from polyhedra. / Oligomeric state: Icosahedral particle / 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: cytoplasmic polyhedrosis virus / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: cytoplasmic polyhedrosis virus
Host (natural)Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 730 Å

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.4 / Details: 10mM PBS
StainingType: NEGATIVE / Details: Sample was not stained
GridDetails: holey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 90 K / Instrument: OTHER / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.75 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 magnification
Legacy - Electron beam tilt params: 0
DetailsLow dose
DateJul 12, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 996 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMIRS / Number images used: 28993
Details645 micrographs that clearly showed signals beyond 6 angstrom in their spectra

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