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- EMDB-1860: Visualising an RNA genome poised for release from its receptor co... -

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Basic information

Entry
Database: EMDB / ID: EMD-1860
TitleVisualising an RNA genome poised for release from its receptor complex.
Map dataThis is a cryo-EM icosahedrally-averaged reconstruction of bacteriophage MS2 bound to an F-pilus with a 5-fold axis.
Sample
  • Sample: Bacteriophage MS2 in complex with F-pilus
  • Virus: Enterobacterio phage MS2 (virus)
  • Organelle or cellular component: F-PILUS
KeywordsMS2 / F-pili / virus-receptor complex
Biological speciesEscherichia coli K-12 (bacteria) / Enterobacterio phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsToropova K / Stockley PG / Ranson NA
CitationJournal: J Mol Biol / Year: 2011
Title: Visualising a viral RNA genome poised for release from its receptor complex.
Authors: Katerina Toropova / Peter G Stockley / Neil A Ranson /
Abstract: We describe the cryo-electron microscopy structure of bacteriophage MS2 bound to its receptor, the bacterial F-pilus. The virus contacts the pilus at a capsid 5-fold vertex, thus locating the surface- ...We describe the cryo-electron microscopy structure of bacteriophage MS2 bound to its receptor, the bacterial F-pilus. The virus contacts the pilus at a capsid 5-fold vertex, thus locating the surface-accessible portion of the single copy of the pilin-binding maturation protein present in virions. This arrangement allows a 5-fold averaged map to be calculated, showing for the first time in any virus-receptor complex the nonuniform distribution of RNA within the capsid. Strikingly, at the vertex that contacts the pilus, a rod of density that may include contributions from both genome and maturation protein sits above a channel that goes through the capsid to the outside. This density is reminiscent of the DNA density observed in the exit channel of double-stranded DNA phages, suggesting that the RNA-maturation protein complex is poised to leave the capsid as the first step of the infection process.
History
DepositionJan 18, 2011-
Header (metadata) releaseFeb 4, 2011-
Map releaseApr 18, 2011-
UpdateApr 18, 2011-
Current statusApr 18, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1860_1860_em...

Downloads & links

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Map

FileDownload / File: emd_1860.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryo-EM icosahedrally-averaged reconstruction of bacteriophage MS2 bound to an F-pilus with a 5-fold axis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 200 pix.
= 392. Å		1.96 Å/pix.
x 200 pix.
= 392. Å		1.96 Å/pix.
x 200 pix.
= 392. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-3.5477 - 5.48773
Average (Standard dev.)-0.00000000263405 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 392 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.961.961.96
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z392.000392.000392.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-3.5485.488-0.000

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Supplemental data

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Sample components

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Entire : Bacteriophage MS2 in complex with F-pilus

EntireName: Bacteriophage MS2 in complex with F-pilus
Components
  • Sample: Bacteriophage MS2 in complex with F-pilus
  • Virus: Enterobacterio phage MS2 (virus)
  • Organelle or cellular component: F-PILUS

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Supramolecule #1000: Bacteriophage MS2 in complex with F-pilus

SupramoleculeName: Bacteriophage MS2 in complex with F-pilus / type: sample / ID: 1000
Oligomeric state: One to one, icosahedral virus bound to filamentous pilus
Number unique components: 2

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Supramolecule #1: Enterobacterio phage MS2

SupramoleculeName: Enterobacterio phage MS2 / type: virus / ID: 1 / Name.synonym: MS2
Details: MS2 in complex with F-pilus, icosahedrally-averaged.
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: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 280 Å / T number (triangulation number): 3

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Supramolecule #2: F-PILUS

SupramoleculeName: F-PILUS / type: organelle_or_cellular_component / ID: 2 / Name.synonym: F-PILUS / Oligomeric state: helical multimer / Recombinant expression: No
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: BW22246

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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: 7.8 / Details: 0.1 M Tris-HCl, 0.5 mM EDTA
GridDetails: Lacey carbon copper mesh grid
VitrificationCryogen name: ETHANE / Chamber temperature: 22 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Double-sided custom pneumatic blotter
Method: 1.6s blot

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 9.88 µm / Number real images: 252 / Average electron dose: 18 e/Å2 / Od range: 1 / Bits/pixel: 16
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

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Image processing

CTF correctionDetails: Phase flipping each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 2739
Final two d classificationNumber classes: 78

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