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- PDB-5lwg: Israeli acute paralysis virus heated to 63 degree - full particle -

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Basic information

Entry
Database: PDB / ID: 5lwg
TitleIsraeli acute paralysis virus heated to 63 degree - full particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / IAPV / Dicistroviridae / full particle / Virus
Function / homologyPicornavirus capsid / Dicistrovirus, capsid-polyprotein, C-terminal / Capsid protein VP4, dicistrovirus / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / picornavirus capsid protein / CRPV capsid protein like / Cricket paralysis virus, VP4 / viral capsid / structural molecule activity ...Picornavirus capsid / Dicistrovirus, capsid-polyprotein, C-terminal / Capsid protein VP4, dicistrovirus / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / picornavirus capsid protein / CRPV capsid protein like / Cricket paralysis virus, VP4 / viral capsid / structural molecule activity / Structural polyprotein / Structural polyprotein / Structural polyprotein / Structural polyprotein / Structural polyprotein
Function and homology information
Specimen sourceIsraeli acute paralysis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsMullapudi, E. / Fuzik, T. / Pridal, A. / Plevka, P.
Funding supportCzech Republic, Germany , 2 items
OrganizationGrant numberCountry
European Research Counciln. 355855Czech Republic
European Molecular Biology Organization#3041Germany
CitationJournal: J. Virol. / Year: 2017
Title: Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus.
Authors: Edukondalu Mullapudi / Tibor Füzik / Antonín Přidal / Pavel Plevka
Abstract: Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse ...Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse disorder in the United States. High-resolution molecular details of the genome delivery mechanism of dicistroviruses are unknown. Here we present a cryo-electron microscopy analysis of IAPV virions induced to release their genomes in vitro We determined structures of full IAPV virions primed to release their genomes to a resolution of 3.3 Å and of empty capsids to a resolution of 3.9 Å. We show that IAPV does not form expanded A particles before genome release as in the case of related enteroviruses of the family Picornaviridae The structural changes observed in the empty IAPV particles include detachment of the VP4 minor capsid proteins from the inner face of the capsid and partial loss of the structure of the N-terminal arms of the VP2 capsid proteins. Unlike the case for many picornaviruses, the empty particles of IAPV are not expanded relative to the native virions and do not contain pores in their capsids that might serve as channels for genome release. Therefore, rearrangement of a unique region of the capsid is probably required for IAPV genome release.
IMPORTANCE: Honeybee populations in Europe and North America are declining due to pressure from pathogens, including viruses. Israeli acute bee paralysis virus (IAPV), a member of the family Dicistroviridae, causes honeybee colony collapse disorder in the United States. The delivery of virus genomes into host cells is necessary for the initiation of infection. Here we present a structural cryo-electron microscopy analysis of IAPV particles induced to release their genomes. We show that genome release is not preceded by an expansion of IAPV virions as in the case of related picornaviruses that infect vertebrates. Furthermore, minor capsid proteins detach from the capsid upon genome release. The genome leaves behind empty particles that have compact protein shells.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 16, 2016 / Release: Nov 30, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 30, 2016Structure modelrepositoryInitial release
1.1Dec 21, 2016Structure modelDatabase references
1.2Feb 8, 2017Structure modelDatabase references
1.3Aug 2, 2017Structure modelData collectionem_software_em_software.name
1.4Oct 17, 2018Structure modelData collection / Refinement descriptionrefine

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Structure visualization

Movie
  • Biological unit as software_defined_assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
C: VP3
B: VP2
D: VP4


Theoretical massNumber of molelcules
Total (without water)90,5754
Polyers90,5754
Non-polymers00
Water0
1
A: VP1
C: VP3
B: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,434,500240
Polyers5,434,500240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA 1.11_b41084.

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Components

#1: Protein/peptide VP1


Mass: 23776.541 Da / Num. of mol.: 1 / Source: (natural) Israeli acute paralysis virus / References: UniProt: G0Z733
#2: Protein/peptide VP3


Mass: 33260.754 Da / Num. of mol.: 1 / Source: (natural) Israeli acute paralysis virus / References: UniProt: G0Z733
#3: Protein/peptide VP2


Mass: 27637.932 Da / Num. of mol.: 1 / Source: (natural) Israeli acute paralysis virus / References: UniProt: B3TZF1, UniProt: B3TZL7*PLUS
#4: Protein/peptide VP4


Mass: 5899.765 Da / Num. of mol.: 1 / Source: (natural) Israeli acute paralysis virus / References: UniProt: B3TZL5, UniProt: R4MP31*PLUS

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Israeli acute paralysis virusList of diseases of the honey bee
Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
Source (natural)Organism: Israeli acute paralysis virus
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRION
Natural hostOrganism: Apis mellifera
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 / Calibrated magnification: 75000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1500
Image scansMovie frames/image: 7 / Used frames/image: 1-7

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2.11particle selectione2boxer.py
2EPU2image acquisition
4CTFFIND4CTF correctionused to determine CTF
5RELIONCTF correctionused to correct CTF
8UCSF Chimera1.11model fitting
10RELION1.4initial Euler assignmentrelion_refine (autorefine)
11RELION1.4final Euler assignmentrelion_refine (autorefine)
12RELION1.4classificationrelion_refine
13RELION1.43D reconstructionrelion_refine (autorefine)
14PHENIX1.10.1model refinementphenix.real_space_refine
15REFMAC5.8.0155model refinementatomsf_electron.lib used for atomsf parameter
Image processingDetails: movie frames were drift aligned by Spider package
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9614 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: initial rigid body fit was done by Chimera, then the model was refined using realspace refinement in Phenix and finaly reciprocal refined in REFMAC.
Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL
RefineCorrelation coeff Fo to Fc: 0.815 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 18.346 / Overall SU ML: 0.288 / Overall ESU R: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 51.121 Å2 / Aniso B11: 0 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0 Å2
Least-squares processR factor R work: 0.31355 / R factor obs: 0.31355 / Highest resolution: 3.2 Å / Lowest resolution: 353.1 Å / Number reflection obs: 239371 / Percent reflection obs: 1
Number of atoms included #1Total: 6373
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0206527
ELECTRON MICROSCOPYr_bond_other_d0.0030.0206093
ELECTRON MICROSCOPYr_angle_refined_deg1.2751.9508914
ELECTRON MICROSCOPYr_angle_other_deg0.9993.00014030
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.4545.000808
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.29924.437293
ELECTRON MICROSCOPYr_dihedral_angle_3_deg10.21115.0001040
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.06215.00036
ELECTRON MICROSCOPYr_chiral_restr0.0720.2001015
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0217420
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0201482
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.2745.1533244
ELECTRON MICROSCOPYr_mcbond_other2.2735.1523243
ELECTRON MICROSCOPYr_mcangle_it4.1887.7244048
ELECTRON MICROSCOPYr_mcangle_other4.1887.7244049
ELECTRON MICROSCOPYr_scbond_it1.8035.1903283
ELECTRON MICROSCOPYr_scbond_other1.8035.1903284
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.4117.7274867
ELECTRON MICROSCOPYr_long_range_B_refined9.70599.79222821
ELECTRON MICROSCOPYr_long_range_B_other9.70599.78922822
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.2 Å / R factor R work: 1.143 / Lowest resolution: 3.283 Å / Number reflection R free: 0 / Number reflection R work: 17573 / Total number of bins used: 20 / Percent reflection obs: 1

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