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- EMDB-5376: Structure of a transcribing cypovirus by cryo-electron microscopy -

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Basic information

Entry
Database: EMDB / ID: EMD-5376
TitleStructure of a transcribing cypovirus by cryo-electron microscopy
Map dataThis is an image of a surface rendered twofold view of transcribing CPV
Sample
  • Sample: transcribing cypovirus
  • Virus: Bombyx mori cypovirus 1
KeywordsdsRNA virus Reoviridae transcribing cypovirus
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 / VP1 / Capsid protein VP1 / Structural protein VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYang C / Ji G / Liu H / Zhang K / Liu G / Sun F / Zhu P / Cheng L
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Cryo-EM structure of a transcribing cypovirus.
Authors: Chongwen Yang / Gang Ji / Hongrong Liu / Kai Zhang / Guangqiao Liu / Fei Sun / Ping Zhu / Lingpeng Cheng /
Abstract: Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription ...Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription cycles. However, how the highly coordinated mRNA transcription and capping process is facilitated by viral capsid proteins is still unknown. Cypovirus provides a good model system for studying the mRNA transcription and capping mechanism of viruses in the family Reoviridae. Here, we report a full backbone model of a transcribing cypovirus built from a near-atomic-resolution density map by cryoelectron microscopy. Compared with the structure of a nontranscribing cypovirus, the major capsid proteins of transcribing cypovirus undergo a series of conformational changes, giving rise to structural changes in the capsid shell: (i) an enlarged capsid chamber, which provides genomic RNA with more flexibility to move within the densely packed capsid, and (ii) a widened peripentonal channel in the capsid shell, which we confirmed to be a pathway for nascent mRNA. A rod-like structure attributable to a partially resolved nascent mRNA was observed in this channel. In addition, conformational change in the turret protein results in a relatively open turret at each fivefold axis. A GMP moiety, which is transferred to 5'-diphosphorylated mRNA during the mRNA capping reaction, was identified in the pocket-like guanylyltransferase domain of the turret protein.
History
DepositionDec 25, 2011-
Header (metadata) releaseJan 11, 2012-
Map releaseMar 26, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j17
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j17
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5376_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5376.map.gz / Format: CCP4 / Size: 695.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered twofold view of transcribing CPV
Voxel sizeX=Y=Z: 1.196 Å
Density
Contour LevelBy AUTHOR: 2.6 / Movie #1: 2.6
Minimum - Maximum-10.0372839 - 15.12658882
Average (Standard dev.)0.0000934 (±1.00155878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-360-3600
Dimensions720720360
Spacing720720360
CellA: 861.12 Å / B: 861.12 Å / C: 430.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1961.1961.196
M x/y/z720720360
origin x/y/z0.0000.0000.000
length x/y/z861.120861.120430.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-360-3600
NC/NR/NS720720360
D min/max/mean-10.03715.1270.000

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Supplemental data

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Sample components

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Entire : transcribing cypovirus

EntireName: transcribing cypovirus
Components
  • Sample: transcribing cypovirus
  • Virus: Bombyx mori cypovirus 1

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Supramolecule #1000: transcribing cypovirus

SupramoleculeName: transcribing cypovirus / type: sample / ID: 1000 / 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: cypovirus / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: cypovirus
Host (natural)Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 650 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: 8
GridDetails: 300 mesh quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Vitrification instrument: FEI Vitrobot Mark IV / Method: blotted for 4s

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 125390 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder: Titan Krios / Specimen holder model: OTHER
TemperatureAverage: 92 K
Detailsparallel beam
DateJul 20, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 845 / Average electron dose: 22 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: IMIRS and ISAF / Number images used: 8000

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