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- EMDB-1431: The three-dimensional structure of genomic RNA in bacteriophage M... -

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Basic information

Entry
Database: EMDB / ID: EMD-1431
TitleThe three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly.
Map dataCryoEM map of the intact virion of bacteriophage MS2
Sample
  • Sample: Bacteriophage MS2
  • Virus: Enterobacterio phage MS2 (virus)
Biological speciesEnterobacterio phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsToropova K / Basnak G / Twarock R / Stockley PG / Ranson NA
CitationJournal: J Mol Biol / Year: 2008
Title: The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly.
Authors: Katerina Toropova / Gabriella Basnak / Reidun Twarock / Peter G Stockley / Neil A Ranson /
Abstract: Using cryo-electron microscopy, single particle image processing and three-dimensional reconstruction with icosahedral averaging, we have determined the three-dimensional solution structure of ...Using cryo-electron microscopy, single particle image processing and three-dimensional reconstruction with icosahedral averaging, we have determined the three-dimensional solution structure of bacteriophage MS2 capsids reassembled from recombinant protein in the presence of short oligonucleotides. We have also significantly extended the resolution of the previously reported structure of the wild-type MS2 virion. The structures of recombinant MS2 capsids reveal clear density for bound RNA beneath the coat protein binding sites on the inner surface of the T=3 MS2 capsid, and show that a short extension of the minimal assembly initiation sequence that promotes an increase in the efficiency of assembly, interacts with the protein capsid forming a network of bound RNA. The structure of the wild-type MS2 virion at approximately 9 A resolution reveals icosahedrally ordered density encompassing approximately 90% of the single-stranded RNA genome. The genome in the wild-type virion is arranged as two concentric shells of density, connected along the 5-fold symmetry axes of the particle. This novel RNA fold provides new constraints for models of viral assembly.
History
DepositionSep 25, 2007-
Header (metadata) releaseSep 26, 2007-
Map releaseMay 16, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.184
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.184
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1431.gif

Downloads & links

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Map

FileDownload / File: emd_1431.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the intact virion of bacteriophage MS2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 256 pix.
= 322.56 Å		1.26 Å/pix.
x 256 pix.
= 322.56 Å		1.26 Å/pix.
x 256 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.794 / Movie #1: 0.184
Minimum - Maximum-1.09669 - 2.45222
Average (Standard dev.)0.0854236 (±0.309357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 322.56 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z322.560322.560322.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ10110173
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.0972.4520.085

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Supplemental data

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Sample components

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Entire : Bacteriophage MS2

EntireName: Bacteriophage MS2 (virus)
Components
  • Sample: Bacteriophage MS2
  • Virus: Enterobacterio phage MS2 (virus)

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Supramolecule #1000: Bacteriophage MS2

SupramoleculeName: Bacteriophage MS2 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacterio phage MS2

SupramoleculeName: Enterobacterio phage MS2 / type: virus / ID: 1 / Name.synonym: MS2 / NCBI-ID: 12022 / Sci species name: Enterobacterio phage MS2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: MS2
Host (natural)Organism: E. coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid / Diameter: 285 Å / T number (triangulation number): 3

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 50 % / Chamber temperature: 22 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: double sided pneumatic blotter
Method: 1.4s blot

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipping each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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