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Yorodumi- EMDB-17053: Head-to-tail double ring assembly from truncated PVY coat protein -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17053 | |||||||||
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Title | Head-to-tail double ring assembly from truncated PVY coat protein | |||||||||
Map data | final trCP double ring cryoEM map after DeepEMhancer post-processing | |||||||||
Sample |
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Keywords | H2T double ring / trCP / 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: 2.93 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_17053.map.gz | 145.7 MB | EMDB map data format | |
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Header (meta data) | emd-17053-v30.xml emd-17053.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17053_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_17053.png | 73.5 KB | ||
Masks | emd_17053_msk_1.map | 163.6 MB | Mask map | |
Filedesc metadata | emd-17053.cif.gz | 5.9 KB | ||
Others | emd_17053_additional_1.map.gz emd_17053_half_map_1.map.gz emd_17053_half_map_2.map.gz | 80.8 MB 151.6 MB 151.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17053 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17053 | HTTPS FTP |
-Validation report
Summary document | emd_17053_validation.pdf.gz | 697.6 KB | Display | EMDB validaton report |
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Full document | emd_17053_full_validation.pdf.gz | 697.2 KB | Display | |
Data in XML | emd_17053_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | emd_17053_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17053 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17053 | HTTPS FTP |
-Related structure data
Related structure data | 8ophMC 8opaC 8opbC 8opcC 8opdC 8opeC 8opfC 8opgC 8opjC 8opkC 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_17053.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | final trCP double ring cryoEM map after DeepEMhancer post-processing | ||||||||||||||||||||||||||||||||||||
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_17053_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: trCP double ring raw cryoEM map (C8)
File | emd_17053_additional_1.map | ||||||||||||
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Annotation | trCP double ring raw cryoEM map (C8) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCP double ring half B cryoEM map
File | emd_17053_half_map_1.map | ||||||||||||
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Annotation | trCP double ring half B cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: trCP double ring half A cryoEM map
File | emd_17053_half_map_2.map | ||||||||||||
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Annotation | trCP double ring half A cryoEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : truncated coat protein (dN49C40) with C-terminal His tag
Entire | Name: truncated coat protein (dN49C40) with C-terminal His tag |
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Components |
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-Supramolecule #1: truncated coat protein (dN49C40) with C-terminal His tag
Supramolecule | Name: truncated coat protein (dN49C40) with C-terminal His tag type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The sample is a mixture of 2 types of filaments, double rings in a head-to-tail arrangement and their association products. |
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Source (natural) | Organism: Potato virus Y strain NTN |
-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: 22.386461 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDG DEQVEYPLKP IVENAKPTLR QIMAHFSDVA EAYIEMRNKK EPYMPRYGLV RNLRDGSLAR YAFDFYEVTS R TPVRAREA ...String: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDG DEQVEYPLKP IVENAKPTLR QIMAHFSDVA EAYIEMRNKK 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 | 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 polymorphic. |
-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: 2862 / 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 |