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- EMDB-4064: single particle reconstruction of slow bee paralysis virus empty ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4064 | |||||||||
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Title | single particle reconstruction of slow bee paralysis virus empty particle | |||||||||
![]() | single particle reconstruction of slow bee paralysis virus empty particle obtained at pH 5.5 | |||||||||
![]() | slow bee paralysis virus != Apis mellifera slow bee paralysis virus
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![]() | icosahedral virus / honebee virus / iflavirus / VIRUS | |||||||||
Function / homology | ![]() host cell membrane / 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 ...host cell membrane / 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 | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | |||||||||
![]() | Kalynych S / Fuzik T / Plevka P | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21 KB | Display | ![]() |
Images | ![]() | 333.6 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lk8MC ![]() 4063C ![]() 5lk7C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | single particle reconstruction of slow bee paralysis virus empty particle obtained at pH 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : slow bee paralysis virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Apis mellifera
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: icosahedral |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.307211 KDa |
Sequence | String: 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 |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.824205 KDa |
Sequence | String: 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 |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 47.62391 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 5.5 / Details: 30 mM Sodium Acetate 50 mM Sodium Chloride |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 2 s.. |
Details | sample was purifed froim natural source and dialyzed overnight into sodium acetate buffer |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 49.7 |
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Output model | ![]() PDB-5lk8: |