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- EMDB-1882: Mutually-induced conformational switching of RNA and coat protein... -

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Basic information

Entry
Database: EMDB / ID: 1882
TitleMutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
KeywordsBacteriophage MS2 / virus assembly / quasi-equivalence / ssRNA virus
SampleBacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and genomic RNA
SourceEnterobacterio phage MS2 / virus / MS2
Enterobacteria phage MS2 / virus / MS2
Map dataThis is a surface-rendered view of a Bacteriophage MS2 virus-like particle composed of purified coat protein and genomic RNA
Methodsingle particle (icosahedral) reconstruction, at 32 A resolution
AuthorsRolfsson O / Toropova K / Ranson NA / Stockley PG
CitationJ. Mol. Biol., 2010, 401, 309-322

J. Mol. Biol., 2010, 401, 309-322 StrPapers
Mutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
Ottar Rolfsson / Katerina Toropova / Neil A Ranson / Peter G Stockley

DateDeposition: Feb 21, 2011 / Header (metadata) release: May 13, 2011 / Map release: May 13, 2011 / Last update: Feb 21, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1882.map.gz (map file in CCP4 format, 31251 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.87 A/pix
= 374. A
200 pix
1.87 A/pix
= 374. A
200 pix
1.87 A/pix
= 374. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.87 A
Density
Contour Level:1 (by emdb), 1 (movie #1):
Minimum - Maximum-4.45316 - 5.72175
Average (Standard dev.)5.57511e-09 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 374 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.871.871.87
M x/y/z200200200
origin x/y/z-0.000-0.000-0.000
length x/y/z374.000374.000374.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-4.4535.7220.000

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Supplemental data

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Sample components

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Entire Bacteriophage MS2 virus-like particles assembled in vitro from pu...

EntireName: Bacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and genomic RNA
Number of components: 2 / Oligomeric State: One capsid to one RNA

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Component #1: virus, Enterobacterio phage MS2

VirusName: Enterobacterio phage MS2 / a.k.a: MS2 / Class: VIRUS-LIKE PARTICLE / Enveloped: No / Empty: No / Isolate: STRAIN
SpeciesSpecies: Enterobacterio phage MS2 / virus / MS2
Source (natural)Host Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Host category: BACTERIA(EUBACTERIA)

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Component #2: nucleic-acid, Single stranded RNA MS2 genome

Nucleic-acidName: Single stranded RNA MS2 genome / a.k.a: Single stranded RNA MS2 genome / Class: RNA
Details: Single stranded RNA MS2 genome was phenol-chloroform extracted from wild type MS2 phage
Structure: SINGLE STRANDED / Synthetic: No
SourceSpecies: Enterobacteria phage MS2 / virus / MS2

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50mM Tris-acetate, 1mM magnesium acetate, 40mM ammonium acetate
pH: 7.6
Support filmQuantifoil R2/1 200 mesh holly carbon grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: 1.6s blot
Details: Vitrification instrument: Double-sided custom pneumatic blotter

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 52750 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Side entry / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: OTHER / Sampling size: 9.88 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 80 / Number of class averages: 19 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection matching / Software: Spider / CTF correction: Phase flip each particle / Resolution: 32 A / Resolution method: FSC 0.5

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