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- PDB-3j17: Structure of a transcribing cypovirus by cryo-electron microscopy -

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Basic information

Entry
Database: PDB / ID: 3j17
TitleStructure of a transcribing cypovirus by cryo-electron microscopy
Components
  • Structural protein VP3Structure
  • Structural protein VP5Structure
  • VP1
KeywordsVIRUS / dsRNA 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
MethodELECTRON MICROSCOPY / single 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, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5376
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  • Superimposition on EM map
  • EMDB-5376
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural protein VP3
B: VP1
C: VP1
D: Structural protein VP5
E: Structural protein VP5


Theoretical massNumber of molelcules
Total (without water)517,6945
Polymers517,6945
Non-polymers00
Water0
1
A: Structural protein VP3
B: VP1
C: VP1
D: Structural protein VP5
E: Structural protein VP5
x 60


Theoretical massNumber of molelcules
Total (without water)31,061,668300
Polymers31,061,668300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Structural protein VP3
B: VP1
C: VP1
D: Structural protein VP5
E: Structural protein VP5
x 5


  • icosahedral pentamer
  • 2.59 MDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)2,588,47225
Polymers2,588,47225
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Structural protein VP3
B: VP1
C: VP1
D: Structural protein VP5
E: Structural protein VP5
x 6


  • icosahedral 23 hexamer
  • 3.11 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)3,106,16730
Polymers3,106,16730
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Structural protein VP3 / Structure


Mass: 120489.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q914N6
#2: Protein VP1


Mass: 148696.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: D3JWE6, UniProt: Q6TS43*PLUS
#3: Protein Structural protein VP5 / Structure


Mass: 49906.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: C6K2M8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: transcribing cypovirus / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Host category: INVERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Bombyx mori
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blotted for 4 seconds, plunged into ethane (FEI Vitrobot Mark IV)
Method: blotted for 4s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 20, 2011 / Details: parallel beam
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 125390 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Titan Krios / Temperature: 92 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 22 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 845
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMIRS3D reconstruction
2ISAF3D reconstruction
CTF correctionDetails: each image
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common lines / Resolution: 4.1 Å / Resolution method: OTHER / Num. of particles: 8000 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms32047 0 0 0 32047

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