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- EMDB-4064: single particle reconstruction of slow bee paralysis virus empty ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4064
Titlesingle particle reconstruction of slow bee paralysis virus empty particle
Map datasingle particle reconstruction of slow bee paralysis virus empty particle obtained at pH 5.5
Sampleslow bee paralysis virus != Apis mellifera

slow bee paralysis virus

  • Virus: Apis mellifera (honey bee)
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
Keywordsicosahedral virus / honebee virus / iflavirus / VIRUS
Function / homology
Function and homology information


viral capsid / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / 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. ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / 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 / 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
Similarity search - Domain/homology
Biological speciesSlow bee paralysis virus / Apis mellifera (honey bee)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsKalynych S / Fuzik T / Plevka P
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Cryo-EM study of slow bee paralysis virus at low pH reveals iflavirus genome release mechanism.
Authors: Sergei Kalynych / Tibor Füzik / Antonín Přidal / Joachim de Miranda / Pavel Plevka /
Abstract: Viruses from the family Iflaviridae are insect pathogens. Many of them, including slow bee paralysis virus (SBPV), cause lethal diseases in honeybees and bumblebees, resulting in agricultural losses. ...Viruses from the family Iflaviridae are insect pathogens. Many of them, including slow bee paralysis virus (SBPV), cause lethal diseases in honeybees and bumblebees, resulting in agricultural losses. Iflaviruses have nonenveloped icosahedral virions containing single-stranded RNA genomes. However, their genome release mechanism is unknown. Here, we show that low pH promotes SBPV genome release, indicating that the virus may use endosomes to enter host cells. We used cryo-EM to study a heterogeneous population of SBPV virions at pH 5.5. We determined the structures of SBPV particles before and after genome release to resolutions of 3.3 and 3.4 Å, respectively. The capsids of SBPV virions in low pH are not expanded. Thus, SBPV does not appear to form "altered" particles with pores in their capsids before genome release, as is the case in many related picornaviruses. The egress of the genome from SBPV virions is associated with a loss of interpentamer contacts mediated by N-terminal arms of VP2 capsid proteins, which result in the expansion of the capsid. Pores that are 7 Å in diameter form around icosahedral threefold symmetry axes. We speculate that they serve as channels for the genome release. Our findings provide an atomic-level characterization of the genome release mechanism of iflaviruses.
History
DepositionJul 21, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseJan 18, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lk8
  • Surface level: 5.01
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lk8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4064.png

Downloads & links

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Map

FileDownload / File: emd_4064.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsingle particle reconstruction of slow bee paralysis virus empty particle obtained at pH 5.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.01 / Movie #1: 5.01
Minimum - Maximum-10.147733000000001 - 16.397504999999999
Average (Standard dev.)-0.000000003409601 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-190-190-190
Dimensions380380380
Spacing380380380
CellA=B=C: 406.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z406.600406.600406.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S213
start NC/NR/NS-190-190-190
NC/NR/NS380380380
D min/max/mean-10.14816.398-0.000

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Supplemental data

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Sample components

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Entire : slow bee paralysis virus

EntireName: slow bee paralysis virus
Components
  • Virus: Apis mellifera (honey bee)
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3

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Supramolecule #1: Apis mellifera

SupramoleculeName: Apis mellifera / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 7460 / Sci species name: Apis mellifera / Sci species strain: 3 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Apis mellifera (honey bee) / Strain: 3
Virus shellShell ID: 1 / Name: icosahedral

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Slow bee paralysis virus
Molecular weightTheoretical: 30.307211 KDa
SequenceString: MERTFTPNVM QPTPLLPTTN DGRVTFGEAF NDLKDLARRY QLYWEGTILE GNLRAIRRNS ALVQLPLYPH GLRIQPDVNN PIWNIMRDG HIPVISSGFR YFRGGLRLRI VVEGLNSCVW VQHHPDRPSI FSRPIIGRYI AAKDAYRNHA YAAYVQNMSV N RTIEVEVP ...String:
MERTFTPNVM QPTPLLPTTN DGRVTFGEAF NDLKDLARRY QLYWEGTILE GNLRAIRRNS ALVQLPLYPH GLRIQPDVNN PIWNIMRDG HIPVISSGFR YFRGGLRLRI VVEGLNSCVW VQHHPDRPSI FSRPIIGRYI AAKDAYRNHA YAAYVQNMSV N RTIEVEVP FYQPGLYGML NASDNNTANS FDRLRFTGLG DLLIGIEGEQ PIPKEGIEIS VYYSIADDFS FNIFCGFPPM VY CDETYSA ATPDLAQYFE DEVTIAQPE

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Slow bee paralysis virus
Molecular weightTheoretical: 29.824205 KDa
SequenceString: MDRPEGSEER TVQTSNVVLG ETNIESQDIA SKEYSPTWDR LASSEVSDEY PMLTDRWLFW KSVKWEVNDS AFGKMLVQEK FPQSWVQMD VNVNNIPRYT NIPNFIPFNI HQYMRADFEV KIYVNPNDFV SGWLIMAFLY QGSEMFDYKL RRNPAALMQM P HVLVNVGA ...String:
MDRPEGSEER TVQTSNVVLG ETNIESQDIA SKEYSPTWDR LASSEVSDEY PMLTDRWLFW KSVKWEVNDS AFGKMLVQEK FPQSWVQMD VNVNNIPRYT NIPNFIPFNI HQYMRADFEV KIYVNPNDFV SGWLIMAFLY QGSEMFDYKL RRNPAALMQM P HVLVNVGA ANEATLKIPY RYVRPFMRCK DILRGDNLIT GVTEPLNMGV LFVEVLIPFR TSAASSAPKS LDVSLFVKMT NA KFTGMVD GSIALLSKPI ALPE

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Slow bee paralysis virus
Molecular weightTheoretical: 47.62391 KDa
SequenceString: DNPPDPTPAK FFVPIPSHSW AHGTNTSEPT NTLRLDGGVV GVGRSDDIGT SDTAISGIIG VYGLLKPFDW NANDTGRNVG GHLLWSMPV HPQVDKDQVI QVMTQSKLTQ YYLPPISVVS SLYAYTRGSI KYKFLFGNNP RHNARLLVAY IPGISSDNRL T LERARNSA ...String:
DNPPDPTPAK FFVPIPSHSW AHGTNTSEPT NTLRLDGGVV GVGRSDDIGT SDTAISGIIG VYGLLKPFDW NANDTGRNVG GHLLWSMPV HPQVDKDQVI QVMTQSKLTQ YYLPPISVVS SLYAYTRGSI KYKFLFGNNP RHNARLLVAY IPGISSDNRL T LERARNSA HVVFSLNEVS EFVFTVPYIT DTMWWPRKYG GPQAAGEFVA PSYICMFILN PLVAMESVPS IVTIVPMIAA GD DFEVAVP AQPAVGLSRN IDVIYPKDSI ISFKSGYFPV YVGSWHSFFD STKAILRYGA VSDHIAQLGN IPANVNRKAF WIV VGDTIK FKTKLDKING TEWFIPEGEY TLGYGVVWRD GAYAYMVPYP LTPLGEKIAQ YTASLLASNT AISQIRPYIP DYIV DSAAS KDNILWSPIE DRLRAQTEWV MAEPE

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 5.5 / Details: 30 mM Sodium Acetate 50 mM Sodium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 2 s..
Detailssample was purifed froim natural source and dialyzed overnight into sodium acetate buffer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Average exposure time: 0.5 sec. / Average electron dose: 21.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5j98


Details: devoid of the protruding domains.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 10350
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Details: RELION 3D refinement was used for angle assignment & refinement
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4)
Details: RELION 3D classification was used for final classification
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 49.7
Output model

PDB-5lk8:
single particle reconstruction of slow bee paralysis virus empty particle

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