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- PDB-6eiw: Sacbrood virus of honeybee empty particle -

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Basic information

Entry
Database: PDB / ID: 6eiw
TitleSacbrood virus of honeybee empty particle
Components
  • minor capsid protein MiCP
  • structural protein VP1
  • structural protein VP2
  • structural protein VP3
KeywordsVIRUS / empty particle / icosahedral virus particle / iflavirus
Function / homology
Function and homology information


host cell membrane / viral capsid / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding ...host cell membrane / viral capsid / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 ...Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Structural protein Vp1 / Genome polyprotein
Similarity search - Component
Biological speciesSacbrood virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsPlevka, P. / Prochazkova, M.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
European Research CouncilFP/2007-2013 (355855) Czech Republic
European Molecular Biology OrganizationIG-3041 Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Virion structure and genome delivery mechanism of sacbrood honeybee virus.
Authors: Michaela Procházková / Tibor Füzik / Karel Škubník / Jana Moravcová / Zorica Ubiparip / Antonín Přidal / Pavel Plevka /
Abstract: Infection by sacbrood virus (SBV) from the family Iflaviridae is lethal to honey bee larvae but only rarely causes the collapse of honey bee colonies. Despite the negative effect of SBV on honey ...Infection by sacbrood virus (SBV) from the family Iflaviridae is lethal to honey bee larvae but only rarely causes the collapse of honey bee colonies. Despite the negative effect of SBV on honey bees, the structure of its particles and mechanism of its genome delivery are unknown. Here we present the crystal structure of SBV virion and show that it contains 60 copies of a minor capsid protein (MiCP) attached to the virion surface. No similar MiCPs have been previously reported in any of the related viruses from the order Picornavirales. The location of the MiCP coding sequence within the SBV genome indicates that the MiCP evolved from a C-terminal extension of a major capsid protein by the introduction of a cleavage site for a virus protease. The exposure of SBV to acidic pH, which the virus likely encounters during cell entry, induces the formation of pores at threefold and fivefold axes of the capsid that are 7 Å and 12 Å in diameter, respectively. This is in contrast to vertebrate picornaviruses, in which the pores along twofold icosahedral symmetry axes are currently considered the most likely sites for genome release. SBV virions lack VP4 subunits that facilitate the genome delivery of many related dicistroviruses and picornaviruses. MiCP subunits induce liposome disruption in vitro, indicating that they are functional analogs of VP4 subunits and enable the virus genome to escape across the endosome membrane into the cell cytoplasm.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.4May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

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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-3881
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: structural protein VP1
B: structural protein VP2
C: structural protein VP3
D: minor capsid protein MiCP


Theoretical massNumber of molelcules
Total (without water)82,5244
Polymers82,5244
Non-polymers00
Water00
1
A: structural protein VP1
B: structural protein VP2
C: structural protein VP3
D: minor capsid protein MiCP
x 60


Theoretical massNumber of molelcules
Total (without water)4,951,440240
Polymers4,951,440240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: structural protein VP1
B: structural protein VP2
C: structural protein VP3
D: minor capsid protein MiCP
x 5


  • icosahedral pentamer
  • 413 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)412,62020
Polymers412,62020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: structural protein VP1
B: structural protein VP2
C: structural protein VP3
D: minor capsid protein MiCP
x 6


  • icosahedral 23 hexamer
  • 495 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)495,14424
Polymers495,14424
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 structural protein VP1


Mass: 26151.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / Plasmid details: Petrusov, CZ / References: UniProt: A0A223DN59, UniProt: Q9WCE9*PLUS
#2: Protein structural protein VP2


Mass: 22563.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / Plasmid details: Petrusov, CZ / References: UniProt: A0A223DN66
#3: Protein structural protein VP3


Mass: 30701.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / Plasmid details: Petrusov, CZ / References: UniProt: A0A2I6HDZ6
#4: Protein/peptide minor capsid protein MiCP


Mass: 3107.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / Plasmid details: Petrusov, CZ / References: UniProt: Q9IGK7

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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: Sacbrood virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sacbrood virus
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellName: capsid / Diameter: 273.94 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaCl1
22.7 mMpotassium chlorideKCl1
310 mMdisodium phosphateNa2HPO41
41.8 mMpotassium phosphateKH2PO41
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: empty particle
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Preliminar grid screening was performed manually on FEI Tecnai F20 (cryo stage).
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 74325 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 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: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16

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Processing

SoftwareName: REFMAC / Version: 5.8.0222 / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4GctfCTF correctionDr. Kai Zhang
7Cootmodel fitting
10RELION2final Euler assignmentrelion_refine_mpi
11RELION2classification
12RELION23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 31804
Details: Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were ...Details: Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were further reconstructed separately.
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10303 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 99.36 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: R-factor
RefinementResolution: 3.87→3.87 Å / Cor.coef. Fo:Fc: 0.919 / SU B: 21.779 / SU ML: 0.29 / ESU R: 0.147
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.37149 --
obs0.37149 584073 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: 88.209 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Total: 5803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0040.0145966
ELECTRON MICROSCOPYr_bond_other_d0.0010.0175179
ELECTRON MICROSCOPYr_angle_refined_deg0.9351.668120
ELECTRON MICROSCOPYr_angle_other_deg0.6061.6312145
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.4795721
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.77921.529327
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.71815940
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.091542
ELECTRON MICROSCOPYr_chiral_restr0.0380.2773
ELECTRON MICROSCOPYr_gen_planes_refined0.0020.026737
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021175
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_it1.4349.2152896
ELECTRON MICROSCOPYr_mcbond_other1.4349.2142895
ELECTRON MICROSCOPYr_mcangle_it2.70113.8143613
ELECTRON MICROSCOPYr_mcangle_other2.713.8153614
ELECTRON MICROSCOPYr_scbond_it0.8369.2013070
ELECTRON MICROSCOPYr_scbond_other0.8359.2023071
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.71713.7564508
ELECTRON MICROSCOPYr_long_range_B_refined4.9626023
ELECTRON MICROSCOPYr_long_range_B_other4.9626024
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.483 43123 -
obs--99.99 %

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