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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
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Structural polyprotein / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesIsraeli acute paralysis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMullapudi, E. / Fuzik, T. / Pridal, A. / Plevka, P.
Funding support Czech Republic, Germany, 2items
OrganizationGrant numberCountry
European Research Counciln. 355855 Czech Republic
European Molecular Biology Organization#3041 Germany
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 ...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.
History
DepositionSep 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.5Dec 11, 2019Group: Other / Category: atom_sites / cell
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] / _cell.Z_PDB

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Structure visualization

Movie
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,5754
Polymers90,5754
Non-polymers00
Water0
1
A: VP1
C: VP3
B: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,434,500240
Polymers5,434,500240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1generate(1), (1), (1)
2generate(-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5)
3generate(1), (-1), (-1)
4generate(0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5)
5generate(0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017)
6generate(-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017)
7generate(-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5)
8generate(-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5)
9generate(-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017)
10generate(0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017)
11generate(-1), (-1), (1)
12generate(-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017)
13generate(-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017)
14generate(-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017)
15generate(-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5)
16generate(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
17generate(-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017)
18generate(-1), (1), (-1)
19generate(-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017)
20generate(-1), (1), (-1)
21generate(-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5)
22generate(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)
23generate(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
24generate(0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017)
25generate(-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5)
26generate(-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017)
27generate(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)
28generate(1), (-1), (-1)
29generate(0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017)
30generate(0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017)
31generate(-1), (1), (-1)
32generate(0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5)
33generate(-1), (-1), (1)
34generate(-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5)
35generate(-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017)
36generate(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
37generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
38generate(0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5)
39generate(0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017)
40generate(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)
41generate(1), (-1), (-1)
42generate(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
43generate(0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017)
44generate(0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017)
45generate(0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5)
46generate(-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017)
47generate(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
48generate(1), (1), (1)
49generate(0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017)
50generate(1), (1), (1)
51generate(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
52generate(-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5)
53generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
54generate(-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017)
55generate(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
56generate(0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017)
57generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
58generate(-1), (-1), (1)
59generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
60generate(-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017)

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Components

#1: Protein VP1


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


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


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


Mass: 5899.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 / 3D 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: all / Source: NATURAL
Source (natural)Organism: Israeli acute paralysis virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / 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 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 75000 X / 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 µm / 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) / Num. of grids imaged: 1 / Num. 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 (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9614 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL
Details: initial rigid body fit was done by Chimera, then the model was refined using realspace refinement in Phenix and finaly reciprocal refined in REFMAC.
RefinementResolution: 3.2→353.1 Å / Cor.coef. Fo:Fc: 0.815 / SU B: 18.346 / SU ML: 0.288 / ESU R: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31355 --
obs0.31355 239371 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.121 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Total: 6373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.026527
ELECTRON MICROSCOPYr_bond_other_d0.0030.026093
ELECTRON MICROSCOPYr_angle_refined_deg1.2751.958914
ELECTRON MICROSCOPYr_angle_other_deg0.999314030
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.4545808
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.29924.437293
ELECTRON MICROSCOPYr_dihedral_angle_3_deg10.211151040
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.0621536
ELECTRON MICROSCOPYr_chiral_restr0.0720.21015
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0217420
ELECTRON MICROSCOPYr_gen_planes_other0.0020.021482
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_it1.8035.193283
ELECTRON MICROSCOPYr_scbond_other1.8035.193284
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
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork1.143 17573 -
Rfree-0 -
obs--100 %

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