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- EMDB-17059: Cross-shaped junction assembly from truncated PVY coat protein wi... -
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Open data
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Basic information
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Title | Cross-shaped junction assembly from truncated PVY coat protein with E150C mutation | |||||||||
![]() | final trCPE150C cubic crossing cryoEM map (O symmetry) after DeepEMHancer post-processing | |||||||||
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![]() | cross-shaped junction / trCP / E150C / Potyvirus / PVY / VIRUS LIKE PARTICLE | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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 | ![]() | 308.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 98.4 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() ![]() ![]() | 170 MB 328 MB 321.7 MB 321.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 936.8 KB | Display | ![]() |
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Full document | ![]() | 936.3 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 31.5 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 | final trCPE150C cubic crossing cryoEM map (O symmetry) after DeepEMHancer post-processing | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.968 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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Density Histograms |
-Additional map: trCPE150C cubic crossing raw cryoEM map (O symmetry)
File | emd_17059_additional_1.map | ||||||||||||
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Annotation | trCPE150C cubic crossing raw cryoEM map (O symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: trCPE150C cubic crossing sharp cryoEM map (O symmetry)
File | emd_17059_additional_2.map | ||||||||||||
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Annotation | trCPE150C cubic crossing sharp cryoEM map (O symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCPE150C cubic crossing half B cryoEM map (O symmetry)
File | emd_17059_half_map_1.map | ||||||||||||
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Annotation | trCPE150C cubic crossing half B cryoEM map (O symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCPE150C cubic crossing half A cryoEM map (O symmetry)
File | emd_17059_half_map_2.map | ||||||||||||
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Annotation | trCPE150C cubic crossing half A cryoEM map (O symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : truncated coat protein (dN49C40) with C-terminal His tag and E150...
Entire | Name: truncated coat protein (dN49C40) with C-terminal His tag and E150C mutation |
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Components |
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-Supramolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and E150...
Supramolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag and E150C mutation type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The sample contains 2 types of filaments, spherical particles and cubic crossings. |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and E150...
Macromolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag and E150C mutation 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 VCNAKPTLRQ IMAHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI ...String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VCNAKPTLRQ IMAHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSE NLYFQGLEHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle 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 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
Details | The sample was very heterogenous. |
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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: 1927 / Average electron dose: 43.0 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 |