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- EMDB-31248: recombinant Alfalfa Mosaic virus coat protein virus-like particle... -

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Basic information

Entry
Database: EMDB / ID: EMD-31248
Titlerecombinant Alfalfa Mosaic virus coat protein virus-like particle (rAMV-CP VLP)
Map dataAlfafa Mosaic virus-like protein T=1
SampleAlfalfa mosaic virus != Alfalfa mosaic virus (strain 425 / isolate Madison)

Alfalfa mosaic virus

  • Virus: Alfalfa mosaic virus (strain 425 / isolate Madison)
    • Protein or peptide: Capsid protein
  • Ligand: water
Keywordsalfalfa mosaic virus / virus-like particle / VIRUS LIKE PARTICLE
Function / homologyCoat protein, Ilarvirus / Ilarvirus coat protein / T=3 icosahedral viral capsid / translational initiation / viral nucleocapsid / RNA binding / Capsid protein
Function and homology information
Biological speciesAlfalfa mosaic virus (strain 425 / isolate Madison)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsJeong H / Lee S
CitationJournal: 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
DepositionApr 27, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7epp
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7epp
  • Imaged by Jmol
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Structure viewerEM map:
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Supplemental images

emd_31248.png

Downloads & links

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Map

FileDownload / File: emd_31248.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlfafa Mosaic virus-like protein T=1
Voxel sizeX=Y=Z: 0.865 Å
Density
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-5.93979 - 10.806115
Average (Standard dev.)-0.0022667055 (±0.27979898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 442.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8650.8650.865
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z442.880442.880442.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-5.94010.806-0.002

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Supplemental data

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Sample components

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Entire : Alfalfa mosaic virus

EntireName: Alfalfa mosaic virus
Components
  • Virus: Alfalfa mosaic virus (strain 425 / isolate Madison)
    • Protein or peptide: Capsid protein
  • Ligand: water

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Supramolecule #1: Alfalfa mosaic virus (strain 425 / isolate Madison)

SupramoleculeName: Alfalfa mosaic virus (strain 425 / isolate Madison) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 12323
Sci species name: Alfalfa mosaic virus (strain 425 / isolate Madison)
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alfalfa mosaic virus (strain 425 / isolate Madison)
Molecular weightTheoretical: 28.373334 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: CMQVWPPIGK KKFETLSYLP DLTGSMSSSQ KKAGGKAGKP TKRSQNYAAL RKAQLPKPPA LKVPVVKPTN TILPQTGCVW QSLGTPLSL SSFNGLGVRF LYSFLKDFAG PRILEEDLIY RMVFSITPSY AGTFCLTDDV TTEDGRAVAH GNPMQEFPHG A FHANEKFG ...String:
CMQVWPPIGK KKFETLSYLP DLTGSMSSSQ KKAGGKAGKP TKRSQNYAAL RKAQLPKPPA LKVPVVKPTN TILPQTGCVW QSLGTPLSL SSFNGLGVRF LYSFLKDFAG PRILEEDLIY RMVFSITPSY AGTFCLTDDV TTEDGRAVAH GNPMQEFPHG A FHANEKFG FELVFTAPTH AGMQNQNFKH SYAVALCLDF DAQPEGSKNP SYRFNEVWVE RKAFPRAGPL RSLITVGLLD EA DDLDRHP RGHHHHHH

UniProtKB: Capsid protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 30 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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