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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | RNA-free helical assembly from truncated PVY coat protein | |||||||||
![]() | trCP helical filament sharp cryoEM map | |||||||||
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![]() | helical / RNA-free / trCP / Potyvirus / PVY / VIRUS LIKE PARTICLE | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.59 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 | ![]() | 20.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 74.6 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() ![]() | 51.4 MB 95.8 MB 95.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8opaC ![]() 8opbC ![]() 8opcC ![]() 8opdC ![]() 8opeC ![]() 8opfC ![]() 8opgC ![]() 8ophC ![]() 8opjC ![]() 8opkC ![]() 8oplC C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | trCP helical filament sharp cryoEM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.976 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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Projections & Slices |
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Density Histograms |
-Additional map: trCP helical filament raw cryoEM map
File | emd_17054_additional_1.map | ||||||||||||
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Annotation | trCP helical filament raw cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCP helical filament half A cryoEM map
File | emd_17054_half_map_1.map | ||||||||||||
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Annotation | trCP helical filament half A cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCP helical filament half B cryoEM map
File | emd_17054_half_map_2.map | ||||||||||||
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Annotation | trCP helical filament half B cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : truncated coat protein (dN49C40) with C-terminal His tag
Entire | Name: truncated coat protein (dN49C40) with C-terminal His tag |
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Components |
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-Supramolecule #1: truncated coat protein (dN49C40) with C-terminal His tag
Supramolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The sample is a mixture of 2 types of filaments, double rings in a head-to-tail arrangement and their association products. |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: truncated coat protein (dN49C40) with C-terminal His tag
Macromolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VENAKPTLRQ IMAHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI ...String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VENAKPTLRQ IMAHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSE NLYFQGLEHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 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 |
Vitrification | Cryogen name: ETHANE |
Details | The sample was polymorphic. |
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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: 2862 / 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 |