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- PDB-3jb4: Structure of Ljungan virus: insight into picornavirus packaging -

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Basic information

Entry
Database: PDB / ID: 3jb4
TitleStructure of Ljungan virus: insight into picornavirus packaging
Components
  • VP0
  • VP1
  • VP3
KeywordsVIRUS / picornaviruses / 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 / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain profile. / LRAT domain / Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLjungan virus 87-012
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhu, L. / Wang, X.X. / Ren, J.S. / Porta, C. / Wenham, H. / Ekstrom, J.-O. / Panjwani, A. / Knowles, N.J. / Kotecha, A. / Siebert, A. ...Zhu, L. / Wang, X.X. / Ren, J.S. / Porta, C. / Wenham, H. / Ekstrom, J.-O. / Panjwani, A. / Knowles, N.J. / Kotecha, A. / Siebert, A. / Lindberg, M. / Fry, E.E. / Rao, Z.H. / Tuthill, T.J. / Stuart, D.I.
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, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6394
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP0
C: VP3


Theoretical massNumber of molelcules
Total (without water)89,0023
Polymers89,0023
Non-polymers00
Water0
1
A: VP1
B: VP0
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,340,137180
Polymers5,340,137180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: VP0
C: VP3
x 5


  • icosahedral pentamer
  • 445 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)445,01115
Polymers445,01115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP0
C: VP3
x 6


  • icosahedral 23 hexamer
  • 534 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)534,01418
Polymers534,01418
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1


Mass: 33091.980 Da / Num. of mol.: 1 / Fragment: UNP residues 504-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ljungan virus 87-012 / Cell line (production host): kidney (Vero) cell / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q8JV21
#2: Protein VP0


Mass: 28237.660 Da / Num. of mol.: 1 / Fragment: UNP residues 1-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ljungan virus 87-012 / Cell line (production host): kidney (Vero) cell / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q8JV21
#3: Protein VP3


Mass: 27672.650 Da / Num. of mol.: 1 / Fragment: UNP residues 260-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ljungan virus 87-012 / Cell line (production host): kidney (Vero) cell / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q8JV21

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ljungan virus (type: 87-012) / Type: VIRUS
Molecular weightValue: 6 MDa / Experimental value: YES
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Rodentia
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Grids with adsorbed viruses were floated on 1% w/v uranyl acetate for 20 seconds.
Specimen supportDetails: 200 mesh gold grid with thin carbon support, glow-discharged in amylamine atmosphere
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 %
Details: Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Feb 2, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm
Astigmatism: Objective lens astigmatism was corrected at 160,000 times magnification.
Specimen holderSpecimen holder model: GATAN HELIUM
Image recordingFilm or detector model: GATAN K2 (4k x 4k)
EM imaging opticsEnergyfilter name: FEI
Image scansNum. digital images: 288

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Processing

EM softwareName: RELION / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5558 / Nominal pixel size: 1.35 Å / Actual pixel size: 1.35 Å / Details: (Single particle--Applied symmetry: I) / Num. of class averages: 20 / Symmetry type: POINT
RefinementResolution: 3.8→129.6 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.962 / SU B: 18.956 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.361
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3133 2715 4.5 %RANDOM
Rwork0.297 ---
obs0.2978 57920 100 %-
Solvent computationSolvent model: NONE
Displacement parametersBiso max: 167.82 Å2 / Biso mean: 70.53 Å2 / Biso min: 9.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-1.75 Å2-0.46 Å2
2--0.87 Å21.22 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 3.8→129.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 0 0 5272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195300
X-RAY DIFFRACTIONr_bond_other_d0.0020.024883
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9227243
X-RAY DIFFRACTIONr_angle_other_deg1.04311134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0465672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70222.818220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84815764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7361532
X-RAY DIFFRACTIONr_chiral_restr0.0920.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216109
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021337
X-RAY DIFFRACTIONr_mcbond_it4.4296.8582697
X-RAY DIFFRACTIONr_mcbond_other4.4296.8582696
X-RAY DIFFRACTIONr_mcangle_it7.77810.283366
LS refinement shellResolution: 3.8→3.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.702 210 -
Rwork0.668 4304 -
all-4514 -
obs--100 %

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