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- EMDB-1432: The three-dimensional structure of genomic RNA in bacteriophage M... -

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Basic information

Entry
Database: EMDB / ID: EMD-1432
TitleThe three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly.
Map dataCryoEM map of TR-MS2
Sample
  • Sample: Recombinant MS2 capsids with TR RNA
  • Protein or peptide: MS2 Capsid
  • RNA: TR RNA
Biological speciesEnterobacterio phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.5 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 26, 2007-
Header (metadata) releaseSep 26, 2007-
Map releaseMay 16, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1432.gif

Downloads & links

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Map

FileDownload / File: emd_1432.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of TR-MS2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.97 Å/pix.
x 160 pix.
= 475.2 Å		2.97 Å/pix.
x 160 pix.
= 475.2 Å		2.97 Å/pix.
x 160 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.97 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.712 / Movie #1: 0.9
Minimum - Maximum-4.94425 - 5.0
Average (Standard dev.)0.01061 (±0.821301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 475.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.972.972.97
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ10110173
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-4.9445.0000.011

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Supplemental data

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Sample components

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Entire : Recombinant MS2 capsids with TR RNA

EntireName: Recombinant MS2 capsids with TR RNA
Components
  • Sample: Recombinant MS2 capsids with TR RNA
  • Protein or peptide: MS2 Capsid
  • RNA: TR RNA

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Supramolecule #1000: Recombinant MS2 capsids with TR RNA

SupramoleculeName: Recombinant MS2 capsids with TR RNA / type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: MS2 Capsid

MacromoleculeName: MS2 Capsid / type: protein_or_peptide / ID: 1 / Name.synonym: MS2 Capsid / Recombinant expression: No
Source (natural)Organism: Enterobacterio phage MS2 (virus) / synonym: Bacteriophage MS2

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Macromolecule #2: TR RNA

MacromoleculeName: TR RNA / type: rna / ID: 2 / Name.synonym: TR-RNA / Details: 19bases / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: Enterobacterio phage MS2 (virus) / synonym: Bacteriophage MS2

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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: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: OTHER / Average electron dose: 15 e/Å2
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
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: 15.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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