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- EMDB-6376: A putative ATPase mediates RNA transcription and capping in a dsR... -

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Basic information

Entry
Database: EMDB / ID: EMD-6376
TitleA putative ATPase mediates RNA transcription and capping in a dsRNA virus
Map dataReconstruction of SG-CPV
Sample
  • Sample: Cytoplasmic polyhedrosis virus with SAM and GTP
  • Virus: Bombyx mori cypovirus 1
KeywordsViral ATPase / histidine-mediated guanylyl transfer / conformational changes / regulation of transcription
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 / Capsid protein VP1 / Structural protein VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYu XK / Jiang JS / Sun JC / Zhou ZH
CitationJournal: Elife / Year: 2015
Title: A putative ATPase mediates RNA transcription and capping in a dsRNA virus.
Authors: Xuekui Yu / Jiansen Jiang / Jingchen Sun / Z Hong Zhou /
Abstract: mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high- ...mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structures of cytoplasmic polyhedrosis virus with bound ligands, we show that the large sub-domain of the guanylyltransferase (GTase) domain of the turret protein (TP) also has an ATP-binding site and is likely an ATPase. S-adenosyl-L-methionine (SAM) acts as a signal and binds the methylase-2 domain of TP to induce conformational change of the viral capsid, which in turn activates the putative ATPase. ATP binding/hydrolysis leads to an enlarged capsid for efficient mRNA synthesis, an open GTase domain for His217-mediated guanylyl transfer, and an open methylase-1 domain for SAM binding and methyl transfer. Taken together, our data support a role of the putative ATPase in mediating the activation of mRNA transcription and capping within the confines of the virus.
History
DepositionJul 5, 2015-
Header (metadata) releaseJul 29, 2015-
Map releaseJul 29, 2015-
UpdateFeb 10, 2016-
Current statusFeb 10, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jb2
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jb2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6376.gif

Downloads & links

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Map

FileDownload / File: emd_6376.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of SG-CPV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 700 pix.
= 772.8 Å		1.1 Å/pix.
x 700 pix.
= 772.8 Å		1.1 Å/pix.
x 700 pix.
= 772.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.104 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-16.67584038 - 27.93304062
Average (Standard dev.)0.08632065 (±1.60225976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-350-350-350
Dimensions700700700
Spacing700700700
CellA=B=C: 772.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1041.1041.104
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z772.800772.800772.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-350-350-350
NC/NR/NS700700700
D min/max/mean-16.67627.9330.086

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Supplemental data

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Sample components

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Entire : Cytoplasmic polyhedrosis virus with SAM and GTP

EntireName: Cytoplasmic polyhedrosis virus with SAM and GTP
Components
  • Sample: Cytoplasmic polyhedrosis virus with SAM and GTP
  • Virus: Bombyx mori cypovirus 1

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Supramolecule #1000: Cytoplasmic polyhedrosis virus with SAM and GTP

SupramoleculeName: Cytoplasmic polyhedrosis virus with SAM and GTP / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Bombyx mori cypovirus 1

SupramoleculeName: Bombyx mori cypovirus 1 / type: virus / ID: 1 / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
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

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification.
DateMar 15, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60535 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.75 mm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: OTHER / Software - Name: IMIRS / Number images used: 46147

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