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

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Entry
Database: EMDB / ID: 6394
TitleStructure of Ljungan virus: insight into picornavirus packaging
Map dataReconstruction of Ljungan virus at 3.8 Angstrom resolution
SampleLjungan virus (type: 87-012):
virus
KeywordsLjungan virus / Picornavirus / assembly / pathogen
Function / homologyPeptidase C3A/C3B, picornaviral / Picornaviridae P3A protein / RNA dependent RNA polymerase / 3C cysteine protease (picornain 3C) / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Helicase, superfamily 3, single-stranded RNA virus / Viral polyprotein, parechovirus P3A / Peptidase S1, PA clan ...Peptidase C3A/C3B, picornaviral / Picornaviridae P3A protein / RNA dependent RNA polymerase / 3C cysteine protease (picornain 3C) / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Helicase, superfamily 3, single-stranded RNA virus / Viral polyprotein, parechovirus P3A / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / viral capsid / ion channel activity / protein complex oligomerization / viral RNA genome replication / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
SourceLjungan virus
Methodsingle particle reconstruction / cryo EM / negative staining / 3.8 Å resolution
AuthorsZhu 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 / Elizabeth E Fry / Zihe Rao / Tobias J Tuthill / David I Stuart
Validation ReportPDB-ID: 3jb4

SummaryFull reportAbout validation report
DateDeposition: Jul 21, 2015 / Header (metadata) release: Sep 23, 2015 / Map release: Oct 21, 2015 / Last update: Oct 21, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
  • 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 models: PDB-3jb4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6394.map.gz (map file in CCP4 format, 182251 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.35 Å/pix.
= 486. Å
360 pix
1.35 Å/pix.
= 486. Å
360 pix
1.35 Å/pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.042 (by author), 0.042 (movie #1):
Minimum - Maximum-0.06862158 - 0.14611761
Average (Standard dev.)0.00119345 (0.01003308)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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Mask #1

Fileemd_6394_msk.map ( map file in CCP4 format, 182251 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::
Annotation detailsThis mask is used to 3D-Autorefinement

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Sample components

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Entire Ljungan virus (type: 87-012)

EntireName: Ljungan virus (type: 87-012) / Number of components: 1
MassTheoretical: 6 MDa / Experimental: 6 MDa / Measured by: Sedimentation

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Component #1: virus, Ljungan virus

VirusName: Ljungan virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 6 MDa / Experimental: 6 MDa
SpeciesSpecies: Ljungan virus
Source (engineered)Expression System: Chlorocebus aethiops (grivet) / Cell of expression system: green monkey kidney (Vero) cells
Source (natural)Host Species: Mus sp. (mice) / Host category: VERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: PBS / pH: 7.4
Support film200 mesh gold grid with thin carbon support, glow-discharged in amylamine atmosphere
StainingGrids with adsorbed viruses were floated on 1% w/v uranyl acetate for 20 seconds.
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Feb 2, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensAstigmatism: Objective lens astigmatism was corrected at 160,000 times magnification.
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: FEI
Specimen HolderModel: GATAN HELIUM
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 288

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 20 / Applied symmetry: I (icosahedral) / Number of projections: 5558
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

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