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- EMDB-12780: MS2 coat protein dimer with 145-AHIVMVDAYKPTKGT-159 SpyTag insert... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-12780
TitleMS2 coat protein dimer with 145-AHIVMVDAYKPTKGT-159 SpyTag insertion VLP displaying fullerene C70-like D5 symmetry
Map datamain volume
Sample
  • Virus: Escherichia virus MS2
    • Protein or peptide: SpyTag modified MS2 bacteriophage capsid protein dimer
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesEscherichia virus MS2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsBiela AP
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2016/20/W/NZ1/00095 Poland
Polish National Science Centre2019/34/A/NZ1/00196 Poland
CitationJournal: Commun Mater / Year: 2022
Title: Programmable polymorphism of a virus-like particle.
Authors: Artur P Biela / Antonina Naskalska / Farzad Fatehi / Reidun Twarock / Jonathan G Heddle /
Abstract: Virus-like particles (VLPs) have significant potential as artificial vaccines and drug delivery systems. The ability to control their size has wide ranging utility but achieving such controlled ...Virus-like particles (VLPs) have significant potential as artificial vaccines and drug delivery systems. The ability to control their size has wide ranging utility but achieving such controlled polymorphism using a single protein subunit is challenging as it requires altering VLP geometry. Here we achieve size control of MS2 bacteriophage VLPs via insertion of amino acid sequences in an external loop to shift morphology to significantly larger forms. The resulting VLP size and geometry is controlled by altering the length and type of the insert. Cryo electron microscopy structures of the new VLPs, in combination with a kinetic model of their assembly, show that the abundance of wild type ( = 3), = 4, D3 and D5 symmetrical VLPs can be biased in this way. We propose a mechanism whereby the insert leads to a change in the dynamic behavior of the capsid protein dimer, affecting the interconversion between the symmetric and asymmetric conformers and thus determining VLP size and morphology.
History
DepositionApr 20, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12780.png

Downloads & links

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Map

FileDownload / File: emd_12780.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31 / Movie #1: 0.31
Minimum - Maximum-0.2603849 - 0.9371213
Average (Standard dev.)0.01843753 (±0.0886475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2600.9370.018

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Supplemental data

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Sample components

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Entire : Escherichia virus MS2

EntireName: Escherichia virus MS2
Components
  • Virus: Escherichia virus MS2
    • Protein or peptide: SpyTag modified MS2 bacteriophage capsid protein dimer

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Supramolecule #1: Escherichia virus MS2

SupramoleculeName: Escherichia virus MS2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 329852 / Sci species name: Escherichia virus MS2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 3.1 MDa
Virus shellShell ID: 1 / Diameter: 340.0 Å

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Macromolecule #1: SpyTag modified MS2 bacteriophage capsid protein dimer

MacromoleculeName: SpyTag modified MS2 bacteriophage capsid protein dimer
type: protein_or_peptide / ID: 1
Details: MS2 coat protein dimer with 145-AHIVMVDAYKPTKGT-159 SpyTag insertion
Enantiomer: LEVO
Source (natural)Organism: Escherichia virus MS2
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASNFTQFVL VDNGGTGDVT VAPSNFANGV AEWISSNSRS QAYKVTCSVR QSSAQNRKYT IKVEVPKVAT QTVGGVELPV AAWRSYLNME LTIPIFATNS DCELIVKAMQ GLLKDGNPIP SAIAANSGIY ANFTQFVLVD NGGTAHIVMV DAYKPTKGTG DVTVAPSNFA ...String:
MASNFTQFVL VDNGGTGDVT VAPSNFANGV AEWISSNSRS QAYKVTCSVR QSSAQNRKYT IKVEVPKVAT QTVGGVELPV AAWRSYLNME LTIPIFATNS DCELIVKAMQ GLLKDGNPIP SAIAANSGIY ANFTQFVLVD NGGTAHIVMV DAYKPTKGTG DVTVAPSNFA NGVAEWISSN SRSQAYKVTC SVRQSSAQNR KYTIKVEVPK VATQTVGGVE LPVAAWRSYL NMELTIPIFA TNSDCELIVK AMQGLLKDGN PIPSAIAANS GIY

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / 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

Particle selectionNumber selected: 1000
CTF correctionSoftware - Name: Warp (ver. 1.0.9)
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Number images used: 4363
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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