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- EMDB-17072: Virus-like Particle based on PVY coat protein with T43C and D136C... -
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Open data
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Basic information
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Title | Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA | |||||||||
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![]() | helical / VLP / ssRNA / Potyvirus / PVY / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.41 Å | |||||||||
![]() | Kavcic L / Kezar A / Podobnik M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Authors: Luka Kavčič / Andreja Kežar / Neža Koritnik / Magda Tušek Žnidarič / Tajda Klobučar / Žiga Vičič / Franci Merzel / Ellie Holden / Justin L P Benesch / Marjetka Podobnik / ![]() ![]() Abstract: The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid ...The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 23 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.8 KB | Display | ![]() |
Images | ![]() | 91.6 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() ![]() | 51.3 MB 95.3 MB 95.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 983.3 KB | Display | ![]() |
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Full document | ![]() | 982.8 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oplMC ![]() 8opaC ![]() 8opbC ![]() 8opcC ![]() 8opdC ![]() 8opeC ![]() 8opfC ![]() 8opgC ![]() 8ophC ![]() 8opjC ![]() 8opkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: #1
File | emd_17072_additional_1.map | ||||||||||||
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-Half map: #2
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Density Histograms |
-Half map: #1
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Sample components
-Entire : Virus-like particles from PVY coat protein with T43C and D136C mu...
Entire | Name: Virus-like particles from PVY coat protein with T43C and D136C mutations |
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Components |
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-Supramolecule #1: Virus-like particles from PVY coat protein with T43C and D136C mu...
Supramolecule | Name: Virus-like particles from PVY coat protein with T43C and D136C mutations type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Monomorphic filaments with helical architecture and encapsidated RNA |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Genome polyprotein (Fragment)
Macromolecule | Name: Genome polyprotein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.925891 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THCVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMCGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE ...String: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THCVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMCGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSA QSRLFGLDGG IS TQEENTE RHTTEDVSPS MHTLLGVKNM UniProtKB: Genome polyprotein |
-Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 27 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.485872 KDa |
Sequence | String: UUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 461 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000 |
Sample stage | Cooling holder cryogen: NITROGEN |