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Yorodumi- PDB-7epp: Recombinant Alfalfa Mosaic virus coat protein virus-like particle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7epp | ||||||
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Title | Recombinant Alfalfa Mosaic virus coat protein virus-like particle (rAMV-CP VLP) | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS LIKE PARTICLE / alfalfa mosaic virus / virus-like particle | ||||||
Function / homology | Coat protein, Ilarvirus / Ilarvirus coat protein / T=3 icosahedral viral capsid / translational initiation / viral nucleocapsid / RNA binding / Capsid protein Function and homology information | ||||||
Biological species | Alfalfa mosaic virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
Authors | Jeong, H. / Lee, S. | ||||||
Citation | Journal: Biochem Biophys Res Commun / Year: 2021 Title: Characterization of alfalfa mosaic virus capsid protein using Cryo-EM. Authors: Hyeongseop Jeong / Youngmin Park / Sooji Song / Kyungmin Min / Jae-Sung Woo / Young-Ho Lee / Eun-Ju Sohn / Sangmin Lee / Abstract: VLPs are virus-like particles that comprise viral capsid proteins that can self-assemble and mimic the shape and size of real viral particles; however, because they do not contain genetic material ...VLPs are virus-like particles that comprise viral capsid proteins that can self-assemble and mimic the shape and size of real viral particles; however, because they do not contain genetic material they cannot infect host cells. VLPs have great potential as safe drug/vehicle candidates; therefore, they are gaining popularity in the field of preventive medicine and therapeutics. Indeed, extensive studies are underway to examine their role as carriers for immunization and as vehicles for delivery of therapeutic agents. Here, we examined the possibility of developing VLP-utilizing technology based on an efficient VLP production process and high-resolution structural analysis. Nicotiana benthamiana was used as an expression platform to produce the coat protein of the alfalfa mosaic virus (AMV-CP). About 250 mg/kg of rAMV-CP was produced from Nicotiana benthamiana leaves. Structural analysis revealed that the oligomeric status of rAMV-CP changed according to the composition and pH of the buffer. Size exclusion chromatography and electron microscopy analysis confirmed the optimal conditions for rAMV-CP VLP formation, and a 2.4 Å resolution structure was confirmed by cryo-EM analysis. Based on the efficient protein production, VLP manufacturing technology, and high-resolution structure presented herein, we suggest that rAMV-CP VLP is a useful platform for development of various new drugs. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 7epp.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7epp.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 7epp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7epp_validation.pdf.gz | 849.7 KB | Display | wwPDB validaton report |
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Full document | 7epp_full_validation.pdf.gz | 849.2 KB | Display | |
Data in XML | 7epp_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7epp_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7epp ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epp | HTTPS FTP |
-Related structure data
Related structure data | 31248MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 28373.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alfalfa mosaic virus (strain 425 / isolate Madison) Gene: ORF3b / Production host: Nicotiana benthamiana (plant) / References: UniProt: P05673 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Alfalfa mosaic virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Alfalfa mosaic virus (strain 425 / isolate Madison) |
Source (recombinant) | Organism: Nicotiana benthamiana (plant) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279755 / Symmetry type: POINT |