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- EMDB-1973: Electron Cryotomography of Measles Virus Reveals how Matrix Prote... -

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Basic information

Entry
Database: EMDB / ID: EMD-1973
TitleElectron Cryotomography of Measles Virus Reveals how Matrix Protein Coats the Ribonucleocapsid Within Intact Virions.
Map dataMeasles virus nucleocapsid filament
Sample
  • Sample: Measles virus matrix-covered ribonucleocapsid, inner helix
  • Protein or peptide: ribonucleocapsid
Keywordsmeasles / matrix / nucleocapsid / ribonucleocapsid / RNP / MCNC
Biological speciesMeasles virus
Methodsubtomogram averaging / cryo EM
AuthorsLiljeroos L / Huiskonen JT / Ora A / Susi P / Butcher SJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Electron cryotomography of measles virus reveals how matrix protein coats the ribonucleocapsid within intact virions.
Authors: Lassi Liljeroos / Juha T Huiskonen / Ari Ora / Petri Susi / Sarah J Butcher /
Abstract: Measles virus is a highly infectious, enveloped, pleomorphic virus. We combined electron cryotomography with subvolume averaging and immunosorbent electron microscopy to characterize the 3D ...Measles virus is a highly infectious, enveloped, pleomorphic virus. We combined electron cryotomography with subvolume averaging and immunosorbent electron microscopy to characterize the 3D ultrastructure of the virion. We show that the matrix protein forms helices coating the helical ribonucleocapsid rather than coating the inner leaflet of the membrane, as previously thought. The ribonucleocapsid is folded into tight bundles through matrix-matrix interactions. The implications for virus assembly are that the matrix already tightly interacts with the ribonucleocapsid in the cytoplasm, providing a structural basis for the previously observed regulation of RNA transcription by the matrix protein. Next, the matrix-covered ribonucleocapsids are transported to the plasma membrane, where the matrix interacts with the envelope glycoproteins during budding. These results are relevant to the nucleocapsid organization and budding of other paramyxoviruses, where isolated matrix has been observed to form helices.
History
DepositionOct 4, 2011-
Header (metadata) releaseOct 21, 2011-
Map releaseOct 28, 2011-
UpdateMay 3, 2012-
Current statusMay 3, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1973_measles...

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Map

FileDownload / File: emd_1973.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMeasles virus nucleocapsid filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.68 Å/pix.
x 72 pix.
= 552.96 Å		7.68 Å/pix.
x 72 pix.
= 552.96 Å		7.68 Å/pix.
x 72 pix.
= 552.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.92032886 - 1.88465607
Average (Standard dev.)0.02041244 (±0.2040793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 552.95996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.687.687.68
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z552.960552.960552.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-1.9201.8850.020

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Supplemental data

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Sample components

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Entire : Measles virus matrix-covered ribonucleocapsid, inner helix

EntireName: Measles virus matrix-covered ribonucleocapsid, inner helix
Components
  • Sample: Measles virus matrix-covered ribonucleocapsid, inner helix
  • Protein or peptide: ribonucleocapsid

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Supramolecule #1000: Measles virus matrix-covered ribonucleocapsid, inner helix

SupramoleculeName: Measles virus matrix-covered ribonucleocapsid, inner helix
type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: ribonucleocapsid

MacromoleculeName: ribonucleocapsid / type: protein_or_peptide / ID: 1 / Name.synonym: ribonucleocapsid / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Measles virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris-HCl, 180 mM NaCl, pH 7.4
GridDetails: C-flat 2/2-2C, holey carbon copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Homemade plunger / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 39400
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsAverage number of projections used in the 3D reconstructions: 772.
Final reconstructionSoftware - Name: IMOD, Bsoft, Jsubtomo

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