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Yorodumi- EMDB-17063: Local refinement of cubic assembly from truncated PVY coat protei... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17063 | ||||||||||||
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Title | Local refinement of cubic assembly from truncated PVY coat protein with K176C mutation | ||||||||||||
Map data | final trCPK176C cubic particle local refinement cryoEM map after DeepEMhancer post-processing (C4) | ||||||||||||
Sample |
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Keywords | cubes / trCP / K176C / Potyvirus / PVY / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein Function and homology information | ||||||||||||
Biological species | Potato virus Y strain NTN | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | ||||||||||||
Authors | Kavcic L / Kezar A / Podobnik M | ||||||||||||
Funding support | Slovenia, Czech Republic, 3 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_17063.map.gz | 692.8 MB | EMDB map data format | |
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Header (meta data) | emd-17063-v30.xml emd-17063.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17063_fsc.xml | 19.8 KB | Display | FSC data file |
Images | emd_17063.png | 123.1 KB | ||
Masks | emd_17063_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-17063.cif.gz | 5.9 KB | ||
Others | emd_17063_additional_1.map.gz emd_17063_additional_2.map.gz emd_17063_half_map_1.map.gz emd_17063_half_map_2.map.gz | 407.5 MB 777.7 MB 763.2 MB 763.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17063 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17063 | HTTPS FTP |
-Validation report
Summary document | emd_17063_validation.pdf.gz | 840.4 KB | Display | EMDB validaton report |
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Full document | emd_17063_full_validation.pdf.gz | 840 KB | Display | |
Data in XML | emd_17063_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | emd_17063_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17063 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17063 | HTTPS FTP |
-Related structure data
Related structure data | 8opkMC 8opaC 8opbC 8opcC 8opdC 8opeC 8opfC 8opgC 8ophC 8opjC 8oplC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17063.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | final trCPK176C cubic particle local refinement cryoEM map after DeepEMhancer post-processing (C4) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
File | emd_17063_msk_1.map | ||||||||||||
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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 |
-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: Potato virus Y strain NTN |
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: Potato virus Y strain NTN / Strain: NTN |
Molecular weight | Theoretical: 22.360424 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | TFS KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |