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Yorodumi- EMDB-17064: Spherical assembly from truncated PVY coat protein with K177E mutation -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17064 | |||||||||
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Title | Spherical assembly from truncated PVY coat protein with K177E mutation | |||||||||
Map data | final trCPK177E spherical particle sharp cryoEM map | |||||||||
Sample |
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Keywords | spherical particle / trCP / K177E / Potyvirus / PVY / VIRUS LIKE PARTICLE | |||||||||
Biological species | Potato virus Y strain NTN | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.75 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_17064.map.gz | 96.9 MB | EMDB map data format | |
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Header (meta data) | emd-17064-v30.xml emd-17064.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17064_fsc.xml | 10.1 KB | Display | FSC data file |
Images | emd_17064.png | 80.3 KB | ||
Masks | emd_17064_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-17064.cif.gz | 5.3 KB | ||
Others | emd_17064_additional_1.map.gz emd_17064_additional_2.map.gz emd_17064_half_map_1.map.gz emd_17064_half_map_2.map.gz | 50.4 MB 25.5 MB 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17064 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17064 | HTTPS FTP |
-Validation report
Summary document | emd_17064_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_17064_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_17064_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_17064_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17064 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17064 | 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_17064.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | final trCPK177E spherical particle sharp cryoEM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17064_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: trCPK177E spherical particle raw cryoEM map
File | emd_17064_additional_1.map | ||||||||||||
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Annotation | trCPK177E spherical particle raw cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: trCPK177E spherical particle ab-initio reconstruction result
File | emd_17064_additional_2.map | ||||||||||||
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Annotation | trCPK177E spherical particle ab-initio reconstruction result | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCPK177E spherical particle half A cryoEM map
File | emd_17064_half_map_1.map | ||||||||||||
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Annotation | trCPK177E spherical particle half A cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCPK177E spherical particle half B cryoEM map
File | emd_17064_half_map_2.map | ||||||||||||
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Annotation | trCPK177E spherical particle 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 K177...
Entire | Name: truncated coat protein (dN49C40) with C-terminal His tag and K177E mutation |
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Components |
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-Supramolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and K177...
Supramolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag and K177E mutation type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Sample contains a mixture of cubic particles and spherical particles. |
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Source (natural) | Organism: Potato virus Y strain NTN |
-Macromolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and K177...
Macromolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag and K177E mutation 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: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VENAKPTLRQ IMAHFSDVAE AYIEMRNKEE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI ...String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VENAKPTLRQ IMAHFSDVAE AYIEMRNKEE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSE NLYFQGLEHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: 501 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000 |