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- EMDB-4989: T=3 MS2 Virus-like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-4989
TitleT=3 MS2 Virus-like particle
Map dataMS2 bacteriophage T=3 virus-like particle map
Sample
  • Virus: Escherichia virus MS2
    • Protein or peptide: Capsid protein
KeywordsMS2 / T=3 / BACTERIOPHAGE / VLP / VIRUS LIKE PARTICLE
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 phage MS2 (virus) / Escherichia virus MS2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
Authorsde Martin Garrido N / Ramlaul K
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust206212_Z_17_Z United Kingdom
Royal Society206212_Z_17_Z United Kingdom
CitationJournal: Mol Microbiol / Year: 2020
Title: Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids.
Authors: Natàlia de Martín Garrido / Michael A Crone / Kailash Ramlaul / Paul A Simpson / Paul S Freemont / Christopher H S Aylett /
Abstract: Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds ...Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 Å and 6 Å respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.
History
DepositionMay 20, 2019-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rrs
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rrs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4989.png

Downloads & links

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Map

FileDownload / File: emd_4989.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMS2 bacteriophage T=3 virus-like particle map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 384 pix.
= 394.637 Å		1.03 Å/pix.
x 384 pix.
= 394.637 Å		1.03 Å/pix.
x 384 pix.
= 394.637 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0277 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.039509207 - 0.109717555
Average (Standard dev.)0.0022433246 (±0.011948504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 394.63678 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.02770052083331.02770052083331.0277005208333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z394.637394.637394.637
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0400.1100.002

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Supplemental data

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Half map: MS2 bacteriophage T=3 virus-like particle unfiltered half-map 1

Fileemd_4989_half_map_1.map
AnnotationMS2 bacteriophage T=3 virus-like particle unfiltered half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MS2 bacteriophage T=3 virus-like particle unfiltered half-map 2

Fileemd_4989_half_map_2.map
AnnotationMS2 bacteriophage T=3 virus-like particle unfiltered half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Capsid protein

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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: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage MS2 (virus)
Molecular weightTheoretical: 13.869659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASNFTQFVL VDNGGTGDVT VAPSNFANGV AEWISSNSRS QAYKVTCSVR QSSAQNRKYT IKVEVPKVAT QTVGGVELPV AAWRSYLNM ELTIPIFATN SDCELIVKAM QGLLKDGNPI PSAIAANSGI Y

UniProtKB: Capsid protein

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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: 7.5 / Details: 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 4 / Number real images: 1040 / Average exposure time: 4.0 sec. / Average electron dose: 80.0 e/Å2
Details: Frames were obtained with a beam-splitter and recorded at 100kx
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.3 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsDose weighting was applied with MotionCor2
Startup modelType of model: EMDB MAP
EMDB ID:

8360

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: Version 2.1
Details: Resolution within a tight mask was 3.9 by FSC 0.143 cut-off while unmasked resolution was 5.
Number images used: 899
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 1 / Software - Name: RELION / Software - details: Version 2.1

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Atomic model buiding 1

Initial modelPDB ID:

5tc1


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsDimers were fitted independently
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6rrs:
T=3 MS2 Virus-like particle

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