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- EMDB-1154: Kelp fly virus: a novel group of insect picorna-like viruses as d... -

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Entry
Database: EMDB / ID: EMD-1154
TitleKelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure.
Map dataThis is a complete icosahedral reconstruction of Kelp fly virus
Sample
  • Sample: Kelp fly virus
  • Virus: Kelp fly virus
Biological speciesKelp fly virus
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsHartley CJ / Greenwood DR / Gilbert RJC
CitationJournal: J Virol / Year: 2005
Title: Kelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure.
Authors: C J Hartley / D R Greenwood / R J C Gilbert / A Masoumi / K H J Gordon / T N Hanzlik / E E Fry / D I Stuart / P D Scotti /
Abstract: The complete genomic sequence of kelp fly virus (KFV), originally isolated from the kelp fly, Chaetocoelopa sydneyensis, has been determined. Analyses of its genomic and structural organization and ...The complete genomic sequence of kelp fly virus (KFV), originally isolated from the kelp fly, Chaetocoelopa sydneyensis, has been determined. Analyses of its genomic and structural organization and phylogeny show that it belongs to a hitherto undescribed group within the picorna-like virus superfamily. The single-stranded genomic RNA of KFV is 11,035 nucleotides in length and contains a single large open reading frame encoding a polypeptide of 3,436 amino acids with 5' and 3' untranslated regions of 384 and 343 nucleotides, respectively. The predicted amino acid sequence of the polypeptide shows that it has three regions. The N-terminal region contains sequences homologous to the baculoviral inhibitor of apoptosis repeat domain, an inhibitor of apoptosis commonly found in animals and in viruses with double-stranded DNA genomes. The second region contains at least two capsid proteins. The third region has three sequence motifs characteristic of replicase proteins of many plant and animal viruses, including a helicase, a 3C chymotrypsin-like protease, and an RNA-dependent RNA polymerase. Phylogenetic analysis of the replicase motifs shows that KFV forms a distinct and distant taxon within the picorna-like virus superfamily. Cryoelectron microscopy and image reconstruction of KFV to a resolution of 15 A reveals an icosahedral structure, with each of its 12 fivefold vertices forming a turret from the otherwise smooth surface of the 20-A-thick capsid. The architecture of the KFV capsid is unique among the members of the picornavirus superfamily for which structures have previously been determined.
History
DepositionAug 17, 2005-
Header (metadata) releaseAug 17, 2005-
Map releaseSep 2, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 22
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 22
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1154.gif

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Map

FileDownload / File: emd_1154.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a complete icosahedral reconstruction of Kelp fly virus
Voxel sizeX=Y=Z: 4.38 Å
Density
Contour Level1: 47.399999999999999 / Movie #1: 22
Minimum - Maximum-119.796000000000006 - 197.164999999999992
Average (Standard dev.)2.09498 (±23.5398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-70-70-69
Dimensions140140140
Spacing140140140
CellA=B=C: 613.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.384.384.38
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z613.200613.200613.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-69
NX/NY/NZ140140140
MAP C/R/S213
start NC/NR/NS-70-70-69
NC/NR/NS140140140
D min/max/mean-119.796197.1652.095

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Supplemental data

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Sample components

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Entire : Kelp fly virus

EntireName: Kelp fly virus
Components
  • Sample: Kelp fly virus
  • Virus: Kelp fly virus

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Supramolecule #1000: Kelp fly virus

SupramoleculeName: Kelp fly virus / type: sample / ID: 1000
Details: The sample displays evidence of a substoichiometric level of turret decoration.
Oligomeric state: One icosahedral virion / Number unique components: 1
Molecular weightExperimental: 4.38 MDa
Method: Volumetrically from the reconstruction and by comparison with the known volume to mass ratio of other insect viruses

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Supramolecule #1: Kelp fly virus

SupramoleculeName: Kelp fly virus / type: virus / ID: 1 / Name.synonym: KFV / NCBI-ID: 340921 / Sci species name: Kelp fly virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: KFV
Host (natural)Organism: Chaetocoelopa sydneyensis (fry) / synonym: INVERTEBRATES
Molecular weightTheoretical: 4.38 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 330 Å
Virus shellShell ID: 2 / Name: Capsid and turrets / Diameter: 450 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

Concentration1.0 mg/mL
BufferpH: 7.2 / Details: 100 mM TRIS, pH 7.2
GridDetails: 300 mesh copper grid, carbon lacey film
VitrificationCryogen name: ETHANE
Method: Blot until grid pulls away from Whatman number 1 paper before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at
DateJun 1, 2001
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.38 µm / Number real images: 27 / Average electron dose: 2 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: By micrograph
Final angle assignmentDetails: SPIDER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER and GAP
Details: Final map was calculated from CTF-corrected reconstruction with unique vertex presented a turret (EMD3965) by applying icosahedral symmetry to an icosahedral asymmetric unit using GAP
Number images used: 3890

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