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Yorodumi- EMDB-17066: Virus-like Particle based on PVY coat protein with L99C and K176C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17066 | |||||||||
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Title | Virus-like Particle based on PVY coat protein with L99C and K176C mutation with stacked-ring architecture | |||||||||
Map data | L99C K176C:VLPr sharp cryoEM map | |||||||||
Sample |
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Keywords | stacked-ring / disulfide-staple / VLP / Potyvirus / PVY / VIRUS LIKE PARTICLE | |||||||||
Biological species | Potato virus Y strain NTN | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Kavcic L / Kezar A / Podobnik M | |||||||||
Funding support | Slovenia, 2 items
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Citation | Journal: Commun Chem / Year: 2024 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 | emd_17066.map.gz | 97.3 MB | EMDB map data format | |
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Header (meta data) | emd-17066-v30.xml emd-17066.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17066_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_17066.png | 123.8 KB | ||
Masks | emd_17066_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-17066.cif.gz | 5.4 KB | ||
Others | emd_17066_additional_1.map.gz emd_17066_half_map_1.map.gz emd_17066_half_map_2.map.gz | 51.6 MB 95.8 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17066 | HTTPS FTP |
-Related structure data
Related structure data | 8opaC 8opbC 8opcC 8opdC 8opeC 8opfC 8opgC 8ophC 8opjC 8opkC 8oplC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17066.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | L99C K176C:VLPr sharp cryoEM map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
File | emd_17066_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: L99C K176C:VLPr raw cryoEM map
File | emd_17066_additional_1.map | ||||||||||||
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Annotation | L99C K176C:VLPr raw cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: L99C K176C:VLPr half A cryoEM map
File | emd_17066_half_map_1.map | ||||||||||||
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Annotation | L99C K176C:VLPr half A cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: L99C K176C:VLPr half B cryoEM map
File | emd_17066_half_map_2.map | ||||||||||||
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Annotation | L99C K176C:VLPr half B cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Virus-like particles from PVY coat protein with L99C and K176C mu...
Entire | Name: Virus-like particles from PVY coat protein with L99C and K176C mutations |
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Components |
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-Supramolecule #1: Virus-like particles from PVY coat protein with L99C and K176C mu...
Supramolecule | Name: Virus-like particles from PVY coat protein with L99C and K176C mutations type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Potato virus Y strain NTN |
-Macromolecule #1: coat protein
Macromolecule | Name: coat protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Potato virus Y strain NTN / Strain: NTN |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQCA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY ...String: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQCA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY IEMRNCKEPY MPRYGLVRNL RDGSLARYAF DFYEVTSRTP VRAREAHIQM KAAALKSAQS RLFGLDGGIS TQEENTERHT TEDVSPSMHT LLGVKNM |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-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 |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 1427 / Average electron dose: 41.3 e/Å2 |