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- EMDB-11117: Human Picobirnavirus D45-CP VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-11117
TitleHuman Picobirnavirus D45-CP VLP
Map dataHPBV delta45 VLP
SampleHuman picobirnavirus != Human picobirnavirus (strain Human/Thailand/Hy005102/-)

Human picobirnavirus

  • Virus: Human picobirnavirus (strain Human/Thailand/Hy005102/-)
    • Protein or peptide: Capsid protein precursor
KeywordsHuman Picobirnavirus / CryoEM / assembly / capsid protein / VIRUS LIKE PARTICLE
Function / homology: / : / Picobirnavirus, Capsid protein / T=3 icosahedral viral capsid / Capsid protein precursor
Function and homology information
Biological speciesHuman picobirnavirus (strain Human/Thailand/Hy005102/-)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsOrtega-Esteban A / Mata CP
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-88736-R Spain
CitationJournal: J Virol / Year: 2020
Title: Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus.
Authors: Álvaro Ortega-Esteban / Carlos P Mata / María J Rodríguez-Espinosa / Daniel Luque / Nerea Irigoyen / Javier M Rodríguez / Pedro J de Pablo / José R Castón /
Abstract: Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and ...Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and replication. This ubiquitous capsid remains structurally undisturbed throughout the viral cycle, isolating the genome to avoid triggering host defense mechanisms. Human picobirnavirus (hPBV) is a dsRNA virus frequently associated with gastroenteritis, although its pathogenicity is yet undefined. Here, we report the cryo-electron microscopy (cryo-EM) structure of hPBV at 2.6-Å resolution. The capsid protein (CP) is arranged in a single-shelled, ∼380-Å-diameter T=1 capsid with a rough outer surface similar to that of dsRNA mycoviruses. The hPBV capsid is built of 60 quasisymmetric CP dimers (A and B) stabilized by domain swapping, and only the CP-A N-terminal basic region interacts with the packaged nucleic acids. hPBV CP has an α-helical domain with a fold similar to that of fungal partitivirus CP, with many domain insertions in its C-terminal half. In contrast to dsRNA mycoviruses, hPBV has an extracellular life cycle phase like complex reoviruses, which indicates that its own CP probably participates in cell entry. Using an reversible assembly/disassembly system of hPBV, we isolated tetramers as possible assembly intermediates. We used atomic force microscopy to characterize the biophysical properties of hPBV capsids with different cargos (host nucleic acids or proteins) and found that the CP N-terminal segment not only is involved in nucleic acid interaction/packaging but also modulates the mechanical behavior of the capsid in conjunction with the cargo. Despite intensive study, human virus sampling is still sparse, especially for viruses that cause mild or asymptomatic disease. Human picobirnavirus (hPBV) is a double-stranded-RNA virus, broadly dispersed in the human population, but its pathogenicity is uncertain. Here, we report the hPBV structure derived from cryo-electron microscopy (cryo-EM) and reconstruction methods using three capsid protein variants (of different lengths and N-terminal amino acid compositions) that assemble as virus-like particles with distinct properties. The hPBV near-atomic structure reveals a quasisymmetric dimer as the structural subunit and tetramers as possible assembly intermediates that coassemble with nucleic acids. Our structural studies and atomic force microscopy analyses indicate that hPBV capsids are potentially excellent nanocages for gene therapy and targeted drug delivery in humans.
History
DepositionJun 2, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z8f
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6z8f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11117.png

Downloads & links

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Map

FileDownload / File: emd_11117.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHPBV delta45 VLP
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.38843393 - 0.60723406
Average (Standard dev.)0.0024647878 (±0.05122596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 426.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.000426.000426.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.3880.6070.002

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Supplemental data

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Sample components

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Entire : Human picobirnavirus

EntireName: Human picobirnavirus
Components
  • Virus: Human picobirnavirus (strain Human/Thailand/Hy005102/-)
    • Protein or peptide: Capsid protein precursor

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Supramolecule #1: Human picobirnavirus (strain Human/Thailand/Hy005102/-)

SupramoleculeName: Human picobirnavirus (strain Human/Thailand/Hy005102/-)
type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 647332
Sci species name: Human picobirnavirus (strain Human/Thailand/Hy005102/-)
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid Protein / Diameter: 380.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein precursor

MacromoleculeName: Capsid protein precursor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human picobirnavirus (strain Human/Thailand/Hy005102/-)
Molecular weightTheoretical: 57.508102 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ESTRNDVAWY ARYPHILEEA TRLPFAYPIG QYYDTGYSVA SATEWSKYVD TSLTIPGVMC VNFTPTPGES YNKNSPINIA AQNVYTYVR HMNSGHANYE QADLMMYLLA MDSLYIFHSY VRKILAISKL YTPVNKYFPR ALLVALGVDP EDVFANQAQW E YFVNMVAY ...String:
ESTRNDVAWY ARYPHILEEA TRLPFAYPIG QYYDTGYSVA SATEWSKYVD TSLTIPGVMC VNFTPTPGES YNKNSPINIA AQNVYTYVR HMNSGHANYE QADLMMYLLA MDSLYIFHSY VRKILAISKL YTPVNKYFPR ALLVALGVDP EDVFANQAQW E YFVNMVAY RAGAFAAPAS MTYYERHAWM SNGLYVDQDV TRAQIYMFKP TMLWKYENLG TTGTKLVPLM MPKAGDNRKL VD FQVLFNN LVSTMLGDED FGIMSGDVFK AFGADGLVKL LAVDSTTMTL PTYDPLILAQ IHSARAVGAP ILETSTLTGF PGR QWQITQ NPDVNNGAII FHPSFGYDGQ DHEELSFRAM CSNMILNLPG EAHSAEMIIE ATRLATMFQV KAVPAGDTSK PVLY LPNGF GTEVVNDYTM ISVDKATPHD LTIHTFFNNI LVPNAKENYV ANLELLNNII QFDWAPQLYL TYGIAQESFG PFAQL NDWT ILTGETLARM HEVCVTSMFD VPQMGFNK

UniProtKB: Capsid protein precursor

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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

BufferpH: 7.5
Component:
ConcentrationFormula
50.0 mMNaClSodium chloride
25.0 mMTrisHCl
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.04 µm / Calibrated defocus min: 0.306 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1990 / Average electron dose: 1.56 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Human Picobirnavirus CP model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 51194

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6z8f:
Human Picobirnavirus D45-CP VLP

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