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- EMDB-17063: Local refinement of cubic assembly from truncated PVY coat protei... -
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Open data
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Basic information
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Title | Local refinement of cubic assembly from truncated PVY coat protein with K176C mutation | ||||||||||||
![]() | final trCPK176C cubic particle local refinement cryoEM map after DeepEMhancer post-processing (C4) | ||||||||||||
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![]() | cubes / trCP / K176C / ![]() ![]() | ||||||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / ![]() ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | 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 | ![]() | 692.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.5 KB 20.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.8 KB | Display | ![]() |
Images | ![]() | 123.1 KB | ||
Masks | ![]() | 824 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 407.5 MB 777.7 MB 763.2 MB 763.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8opkMC ![]() 8opaC ![]() 8opbC ![]() 8opcC ![]() 8opdC ![]() 8opeC ![]() 8opfC ![]() 8opgC ![]() 8ophC ![]() 8opjC ![]() 8oplC C: citing same article ( M: atomic model generated by this map |
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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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Annotation | final trCPK176C cubic particle local refinement cryoEM map after DeepEMhancer post-processing (C4) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 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: trCPK176C cubic particle local refinement raw cryoEM map (C4)
File | emd_17063_additional_1.map | ||||||||||||
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Annotation | trCPK176C cubic particle local refinement raw cryoEM map (C4) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: trCPK176C cubic particle local refinement sharp cryoEM map (C4)
File | emd_17063_additional_2.map | ||||||||||||
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Annotation | trCPK176C cubic particle local refinement sharp cryoEM map (C4) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCPK176C cubic particle local refinement half A cryoEM map
File | emd_17063_half_map_1.map | ||||||||||||
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Annotation | trCPK176C cubic particle local refinement half A cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCPK176C cubic particle local refinement half B cryoEM map
File | emd_17063_half_map_2.map | ||||||||||||
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Annotation | trCPK176C cubic particle local refinement 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 and K176...
Entire | Name: truncated coat protein (dN49C40) with C-terminal His tag and K176C mutation |
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Components |
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-Supramolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and K176...
Supramolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag and K176C mutation type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: structurally homogenous cubic particles |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.315 MDa |
-Macromolecule #1: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.360424 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDG DEQVEYPLKP IVENAKPTLR QIMAHFSDVA EAYIEMRNCK EPYMPRYGLV RNLRDGSLAR YAFDFYEVTS R TPVRAREA ...String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDG DEQVEYPLKP IVENAKPTLR QIMAHFSDVA EAYIEMRNCK EPYMPRYGLV RNLRDGSLAR YAFDFYEVTS R TPVRAREA HIQMKAAALK SENLYFQGLE HHHHHH UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 4 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 |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 9480 / Average exposure time: 4.0 sec. / Average electron dose: 32.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |