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- EMDB-5926: Identification of the active sites in the methyltransferases of a... -

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Basic information

Entry
Database: EMDB / ID: EMD-5926
TitleIdentification of the active sites in the methyltransferases of a transcribing dsRNA virus
Map dataReconstruction of transcribing cypovirus
Sample
  • Sample: transcribing cypovirus
  • Virus: Bombyx mori cypovirus 1
KeywordsdsRNA virus / Reoviridae / RNA capping / RNA methyltransferase
Function / homology: / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / Structural protein VP3
Function and homology information
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhu B / Yang C / Liu H / Cheng L / Song F / Zeng S / Huang X / Ji G / Zhu P
CitationJournal: J Mol Biol / Year: 2014
Title: Identification of the active sites in the methyltransferases of a transcribing dsRNA virus.
Authors: Bin Zhu / Chongwen Yang / Hongrong Liu / Lingpeng Cheng / Feng Song / Songjun Zeng / Xiaojun Huang / Gang Ji / Ping Zhu /
Abstract: Many double-stranded RNA (dsRNA) viruses are capable of transcribing and capping RNA within a stable icosahedral viral capsid. The turret of turreted dsRNA viruses belonging to the family Reoviridae ...Many double-stranded RNA (dsRNA) viruses are capable of transcribing and capping RNA within a stable icosahedral viral capsid. The turret of turreted dsRNA viruses belonging to the family Reoviridae is formed by five copies of the turret protein, which contains domains with both 7-N-methyltransferase and 2'-O-methyltransferase activities, and serves to catalyze the methylation reactions during RNA capping. Cypovirus of the family Reoviridae provides a good model system for studying the methylation reactions in dsRNA viruses. Here, we present the structure of a transcribing cypovirus to a resolution of ~3.8Å by cryo-electron microscopy. The binding sites for both S-adenosyl-L-methionine and RNA in the two methyltransferases of the turret were identified. Structural analysis of the turret in complex with RNA revealed a pathway through which the RNA molecule reaches the active sites of the two methyltransferases before it is released into the cytoplasm. The pathway shows that RNA capping reactions occur in the active sites of different turret protein monomers, suggesting that RNA capping requires concerted efforts by at least three turret protein monomers. Thus, the turret structure provides novel insights into the precise mechanisms of RNA methylation.
History
DepositionMar 19, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseOct 8, 2014-
UpdateOct 15, 2014-
Current statusOct 15, 2014Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 20
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 20
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6q
  • Surface level: 20
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5926.gif

Downloads & links

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Map

FileDownload / File: emd_5926.map.gz / Format: CCP4 / Size: 454 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of transcribing cypovirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 313 pix.
= 374.348 Å		1.2 Å/pix.
x 624 pix.
= 746.304 Å		1.2 Å/pix.
x 624 pix.
= 746.304 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: 1.196 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 20.0 / Movie #1: 20
Minimum - Maximum-104.620079039999993 - 114.121688840000004
Average (Standard dev.)1.2016679 (±10.38885307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-312-3120
Dimensions624624313
Spacing624624313
CellA: 746.304 Å / B: 746.304 Å / C: 374.348 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1961.1961.196
M x/y/z624624313
origin x/y/z0.0000.0000.000
length x/y/z746.304746.304374.348
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-312-3120
NC/NR/NS624624313
D min/max/mean-104.620114.1221.202

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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: 1

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Supramolecule #1: Bombyx mori cypovirus 1

SupramoleculeName: Bombyx mori cypovirus 1 / type: virus / ID: 1 / Name.synonym: BmCPV / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: BmCPV
Host (natural)Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateOct 10, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 4000
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 125390 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: IMIRS, ISAF, EMAN / Number images used: 30000

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