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- EMDB-5353: The 3D volume of the Birnavirus, Espirito Santo Virus. -

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Basic information

Entry
Database: EMDB / ID: EMD-5353
TitleThe 3D volume of the Birnavirus, Espirito Santo Virus.
Map dataThis is the 3D volume of the Birnavirus, Espirito Santo Virus
Sample
  • Sample: Espirito Santo Virus
  • Virus: Espirito Santo virus
KeywordsBirnavirus / cryoEM
Biological speciesEspirito Santo virus
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsVancini R / Paredes A / Ribeiro M / Blackburn K / Ferreira D / Kononchik J / Hernandez R / Brown D
CitationJournal: J Virol / Year: 2012
Title: Espirito Santo virus: a new birnavirus that replicates in insect cells.
Authors: Ricardo Vancini / Angel Paredes / Mariana Ribeiro / Kevin Blackburn / Davis Ferreira / Joseph P Kononchik / Raquel Hernandez / Dennis Brown /
Abstract: Espirito Santo virus (ESV) is a newly discovered virus recovered as contamination in a sample of a virulent strain of dengue-2 virus (strain 44/2), which was recovered from a patient in the state of ...Espirito Santo virus (ESV) is a newly discovered virus recovered as contamination in a sample of a virulent strain of dengue-2 virus (strain 44/2), which was recovered from a patient in the state of Espirito Santo, Brazil, and amplified in insect cells. ESV was found to be dependent upon coinfection with a virulent strain of dengue-2 virus and to replicate in C6/36 insect cells but not in mammalian Vero cells. A sequence of the genome has been produced by de novo assembly and was not found to match to any known viral sequence. An incomplete match to the nucleotide sequence of the RNA-dependent RNA polymerase from Drosophila X virus (DXV), another birnavirus, could be detected. Mass spectrometry analysis of ESV proteins found no matches in the protein data banks. However, peptides recovered by mass spectrometry corresponded to the de novo-assembled sequence by BLAST analysis. The composition and three-dimensional structure of ESV are presented, and its sequence is compared to those of other members of the birnavirus family. Although the virus was found to belong to the family Birnaviridae, biochemical and sequence information for ESV differed from that of DXV, the representative species of the genus Entomobirnavirus. Thus, significant differences underscore the uniqueness of this infectious agent, and its relationship to the coinfecting virus is discussed.
History
DepositionNov 14, 2011-
Header (metadata) releaseNov 28, 2011-
Map releaseJan 23, 2012-
UpdateFeb 7, 2012-
Current statusFeb 7, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5353_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5353.map.gz / Format: CCP4 / Size: 141.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the 3D volume of the Birnavirus, Espirito Santo Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.29 Å/pix.
x 336 pix.
= 769.44 Å		2.29 Å/pix.
x 336 pix.
= 769.44 Å		2.29 Å/pix.
x 336 pix.
= 769.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.28 / Movie #1: 1.28
Minimum - Maximum-8.09881592 - 9.754880910000001
Average (Standard dev.)0.14425604 (±1.28415811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-168-168-168
Dimensions336336336
Spacing336336336
CellA=B=C: 769.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.292.292.29
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z769.440769.440769.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-168-168-168
NC/NR/NS336336336
D min/max/mean-8.0999.7550.144

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Supplemental data

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Sample components

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Entire : Espirito Santo Virus

EntireName: Espirito Santo Virus
Components
  • Sample: Espirito Santo Virus
  • Virus: Espirito Santo virus

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Supramolecule #1000: Espirito Santo Virus

SupramoleculeName: Espirito Santo Virus / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1

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Supramolecule #1: Espirito Santo virus

SupramoleculeName: Espirito Santo virus / type: virus / ID: 1 / Name.synonym: ESV / NCBI-ID: 1127767 / Sci species name: Espirito Santo virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: ESV
Host (natural)Organism: Homo sapiens (human) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 750 Å / T number (triangulation number): 13

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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: 7.5 / Details: 1.5% glutaraldehyde, 20mM HEPES, pH 7.5
GridDetails: 400 mesh copper grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Home made plunger. Vitrification carried out using home made lacey carbon films according to previously published protocols
Method: Applied specimen to lacey carbon grids, blotted from behind and plunged into cryogen after 2-3 seconds

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Electron microscopy

MicroscopeFEI POLARA 300
Alignment procedureLegacy - Astigmatism: corrected using power spectrum
DateJun 20, 2010
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 199 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 39000
Sample stageSpecimen holder: Screw ring cartidge / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using e2boxer.py in the EMAN2 suite of programs
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5928

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