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- EMDB-7596: Promotion of Virus Assembly and Organization by the Measles Virus... -

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Basic information

Entry
Database: EMDB / ID: EMD-7596
TitlePromotion of Virus Assembly and Organization by the Measles Virus Matrix Protein: RNP average (Class 2)
Map dataRNP average of measles virus, Class 2
Sample
  • Virus: Measles virus
Biological speciesMeasles virus
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsKe Z / Strauss JD / Hampton CM / Dillard RS / Wright ER
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114561 United States
National Science Foundation (NSF, United States)0923395 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI101775 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01HD079327 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI083402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM112517 United States
CitationJournal: Nat Commun / Year: 2018
Title: Promotion of virus assembly and organization by the measles virus matrix protein.
Authors: Zunlong Ke / Joshua D Strauss / Cheri M Hampton / Melinda A Brindley / Rebecca S Dillard / Fredrick Leon / Kristen M Lamb / Richard K Plemper / Elizabeth R Wright /
Abstract: Measles virus (MeV) remains a major human pathogen, but there are presently no licensed antivirals to treat MeV or other paramyxoviruses. Here, we use cryo-electron tomography (cryo-ET) to elucidate ...Measles virus (MeV) remains a major human pathogen, but there are presently no licensed antivirals to treat MeV or other paramyxoviruses. Here, we use cryo-electron tomography (cryo-ET) to elucidate the principles governing paramyxovirus assembly in MeV-infected human cells. The three-dimensional (3D) arrangement of the MeV structural proteins including the surface glycoproteins (F and H), matrix protein (M), and the ribonucleoprotein complex (RNP) are characterized at stages of virus assembly and budding, and in released virus particles. The M protein is observed as an organized two-dimensional (2D) paracrystalline array associated with the membrane. A two-layered F-M lattice is revealed suggesting that interactions between F and M may coordinate processes essential for MeV assembly. The RNP complex remains associated with and in close proximity to the M lattice. In this model, the M lattice facilitates the well-ordered incorporation and concentration of the surface glycoproteins and the RNP at sites of virus assembly.
History
DepositionMar 19, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseMay 9, 2018-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.75
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.75
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7596.png

Downloads & links

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Map

FileDownload / File: emd_7596.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNP average of measles virus, Class 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.88 Å/pix.
x 96 pix.
= 564.48 Å		5.88 Å/pix.
x 96 pix.
= 564.48 Å		5.88 Å/pix.
x 96 pix.
= 564.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.75 / Movie #1: 1.75
Minimum - Maximum-8.3388195 - 8.561133
Average (Standard dev.)0.00000000500 (±0.99999946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 564.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.885.885.88
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z564.480564.480564.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-8.3398.5610.000

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Supplemental data

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Sample components

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Entire : Measles virus

EntireName: Measles virus
Components
  • Virus: Measles virus

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Supramolecule #1: Measles virus

SupramoleculeName: Measles virus / type: virus / ID: 1 / Parent: 0 / Details: Measles virus RNP average, class 2 / NCBI-ID: 11234 / Sci species name: Measles virus / Sci species strain: Edmonston / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3
Detailsmeasles virus infected cells

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Digitization - Dimensions - Width: 5080 pixel / Digitization - Dimensions - Height: 3768 pixel / Digitization - Frames/image: 1-8 / Average exposure time: 0.4 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 20000
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 78.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.6923 °
Applied symmetry - Helical parameters - Axial symmetry: C13 (13 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.11.0 alpha) / Number subtomograms used: 1084
ExtractionNumber tomograms: 2 / Number images used: 225 / Method: volumes picked manually in IMOD slicer window / Software - Name: IMOD (ver. 4.9.4)
CTF correctionSoftware - Name: eTomo (ver. 4.9.4)
Final 3D classificationSoftware - Name: PEET (ver. 1.11.0 alpha) / Software - details: PCA analysis and k-means clustering
Final angle assignmentType: NOT APPLICABLE

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