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- EMDB-6394: Structure of Ljungan virus: insight into picornavirus packaging -

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Basic information

Entry
Database: EMDB / ID: EMD-6394
TitleStructure of Ljungan virus: insight into picornavirus packaging
Map dataReconstruction of Ljungan virus at 3.8 Angstrom resolution
Sample
  • Sample: Ljungan virus (type: 87-012)
  • Virus: Ljungan virus
KeywordsLjungan virus / Picornavirus / assembly / pathogen
Function / homology
Function and homology information


host cell nucleolus / host cell Golgi membrane / picornain 3C / host cell cytoplasmic vesicle membrane / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity ...host cell nucleolus / host cell Golgi membrane / picornain 3C / host cell cytoplasmic vesicle membrane / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain profile. / LRAT domain / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein ...Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain profile. / LRAT domain / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesLjungan virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.8 Å
AuthorsZhu L / Wang XX / Ren JS / Porta C / Wenham H / Ekstrom J-O / Panjwani A / Knowles NJ / Kotecha A / Siebert A ...Zhu L / Wang XX / Ren JS / Porta C / Wenham H / Ekstrom J-O / Panjwani A / Knowles NJ / Kotecha A / Siebert A / Lindberg M / Fry EE / Rao ZH / Tuthill TJ / Stuart DI
CitationJournal: Nat Commun / Year: 2015
Title: Structure of Ljungan virus provides insight into genome packaging of this picornavirus.
Authors: Ling Zhu / Xiangxi Wang / Jingshan Ren / Claudine Porta / Hannah Wenham / Jens-Ola Ekström / Anusha Panjwani / Nick J Knowles / Abhay Kotecha / C Alistair Siebert / A Michael Lindberg / ...Authors: Ling Zhu / Xiangxi Wang / Jingshan Ren / Claudine Porta / Hannah Wenham / Jens-Ola Ekström / Anusha Panjwani / Nick J Knowles / Abhay Kotecha / C Alistair Siebert / A Michael Lindberg / Elizabeth E Fry / Zihe Rao / Tobias J Tuthill / David I Stuart /
Abstract: Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are ...Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-Å resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.
History
DepositionJul 21, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseOct 21, 2015-
UpdateOct 21, 2015-
Current statusOct 21, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jb4
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jb4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6394.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Ljungan virus at 3.8 Angstrom resolution
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.06862158 - 0.14611761
Average (Standard dev.)0.00119345 (±0.01003308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0690.1460.001

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Supplemental data

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Segmentation: This mask is used to 3D-Autorefinement

AnnotationThis mask is used to 3D-Autorefinement
Fileemd_6394_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Ljungan virus (type: 87-012)

EntireName: Ljungan virus (type: 87-012)
Components
  • Sample: Ljungan virus (type: 87-012)
  • Virus: Ljungan virus

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Supramolecule #1000: Ljungan virus (type: 87-012)

SupramoleculeName: Ljungan virus (type: 87-012) / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 6 MDa / Theoretical: 6 MDa / Method: Sedimentation

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Supramolecule #1: Ljungan virus

SupramoleculeName: Ljungan virus / type: virus / ID: 1 / NCBI-ID: 172314 / Sci species name: Ljungan virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus sp. (mice) / synonym: VERTEBRATES
Host systemOrganism: Chlorocebus aethiops (grivet) / Recombinant cell: green monkey kidney (Vero) cells
Molecular weightExperimental: 6 MDa / Theoretical: 6 MDa
Virus shellShell ID: 1 / Diameter: 320 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: PBS
StainingType: NEGATIVE
Details: Grids with adsorbed viruses were floated on 1% w/v uranyl acetate for 20 seconds.
GridDetails: 200 mesh gold grid with thin carbon support, glow-discharged in amylamine atmosphere
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder model: GATAN HELIUM
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 160,000 times magnification.
DateFeb 2, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 288
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final two d classificationNumber classes: 20
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 5558

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