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- EMDB-6321: Genome and RdRp structures within the capsid of transcribing cypo... -

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Basic information

Entry
Database: EMDB / ID: EMD-6321
TitleGenome and RdRp structures within the capsid of transcribing cypoviruses
Map datasymmetry-mismatch reconstruction of transcribing cypoviruses
Sample
  • Sample: transcribing cypoviruses
  • Virus: Bombyx mori cypovirus 1
Keywordstranscribing cypoviruses / RNA-dependent RNA polymerases / genome structure / dsRNA virus
Function / homology
Function and homology information


viral genome replication / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
: / : / CPV, RNA-directed RNA polymerase, N-terminal / CPV, RNA-directed RNA polymerase, central polymerase domain / CPV, RNA-directed RNA polymerase, C-terminal / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsLiu H / Cheng L
CitationJournal: Science / Year: 2015
Title: Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus.
Authors: Hongrong Liu / Lingpeng Cheng /
Abstract: Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps ...Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures.
History
DepositionApr 18, 2015-
Header (metadata) releaseJun 10, 2015-
Map releaseOct 28, 2015-
UpdateAug 31, 2016-
Current statusAug 31, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3ja4
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3ja4
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3ja4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6321.jpg

Downloads & links

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Map

FileDownload / File: emd_6321.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsymmetry-mismatch reconstruction of transcribing cypoviruses
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.39 Å/pix.
x 300 pix.
= 717.6 Å		2.39 Å/pix.
x 300 pix.
= 717.6 Å		2.39 Å/pix.
x 300 pix.
= 717.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.392 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 15.0 / Movie #1: 15
Minimum - Maximum-15.513099670000001 - 36.009845730000002
Average (Standard dev.)2.76888371 (±9.63803673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 717.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.3922.3922.392
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z717.600717.600717.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-15.51336.0102.769

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Supplemental data

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Segmentation: 4.8 angstrom resolution structure of RNA-dependent RNA polymerases...

Annotation4.8 angstrom resolution structure of RNA-dependent RNA polymerases within transcribing cypoviruses
Fileemd_6321_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: 6 angstron resolution turret structure masked from whole virus

Annotation6 angstron resolution turret structure masked from whole virus
Fileemd_6321_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : transcribing cypoviruses

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

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Supramolecule #1000: transcribing cypoviruses

SupramoleculeName: transcribing cypoviruses / 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 / 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: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 715 Å

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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 / 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)
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 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

DetailsSymmetry-mismatch reconstruction of icosahedral virus without symmetry imposed
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Number images used: 36000

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