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- EMDB-2391: Human Respiratory Syncytial Virus ribonucleocapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2391
TitleHuman Respiratory Syncytial Virus ribonucleocapsid
Map dataSubtomogram average of hRSV nucleocapsid
Sample
  • Sample: Human Respiratory Syncytial Virus ribonucleocapsid
  • Virus: Human respiratory syncytial virus
KeywordsRSV / RNP / nucleocapsid
Biological speciesHuman respiratory syncytial virus
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsLiljeroos L / Krzyzaniak MA / Helenius A / Butcher SJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Architecture of respiratory syncytial virus revealed by electron cryotomography.
Authors: Lassi Liljeroos / Magdalena Anna Krzyzaniak / Ari Helenius / Sarah Jane Butcher /
Abstract: Human respiratory syncytial virus is a human pathogen that causes severe infection of the respiratory tract. Current information about the structure of the virus and its interaction with host cells ...Human respiratory syncytial virus is a human pathogen that causes severe infection of the respiratory tract. Current information about the structure of the virus and its interaction with host cells is limited. We carried out an electron cryotomographic characterization of cell culture-grown human respiratory syncytial virus to determine the architecture of the virion. The particles ranged from 100 nm to 1,000 nm in diameter and were spherical, filamentous, or a combination of the two. The filamentous morphology correlated with the presence of a cylindrical matrix protein layer linked to the inner leaflet of the viral envelope and with local ordering of the glycoprotein spikes. Recombinant viruses with only the fusion protein in their envelope showed that these glycoproteins were predominantly in the postfusion conformation, but some were also in the prefusion form. The ribonucleocapsids were left-handed, randomly oriented, and curved inside the virions. In filamentous particles, they were often adjacent to an intermediate layer of protein assigned to M2-1 (an envelope-associated protein known to mediate association of ribonucleocapsids with the matrix protein). Our results indicate important differences in structure between the Paramyxovirinae and Pneumovirinae subfamilies within the Paramyxoviridae, and provide fresh insights into host cell exit of a serious pathogen.
History
DepositionJun 3, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 3, 2013-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2391.tif

Downloads & links

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Map

FileDownload / File: emd_2391.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of hRSV nucleocapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.68 Å/pix.
x 64 pix.
= 491.52 Å		7.68 Å/pix.
x 64 pix.
= 491.52 Å		7.68 Å/pix.
x 64 pix.
= 491.52 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: 0.7 / Movie #1: 0.7
Minimum - Maximum-9.509798050000001 - 7.48117113
Average (Standard dev.)0.0 (±0.99999988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.687.687.68
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z491.520491.520491.520
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-9.5107.481-0.000

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Supplemental data

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Sample components

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Entire : Human Respiratory Syncytial Virus ribonucleocapsid

EntireName: Human Respiratory Syncytial Virus ribonucleocapsid
Components
  • Sample: Human Respiratory Syncytial Virus ribonucleocapsid
  • Virus: Human respiratory syncytial virus

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Supramolecule #1000: Human Respiratory Syncytial Virus ribonucleocapsid

SupramoleculeName: Human Respiratory Syncytial Virus ribonucleocapsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human respiratory syncytial virus

SupramoleculeName: Human respiratory syncytial virus / type: virus / ID: 1 / Name.synonym: ribonucleocapsid / NCBI-ID: 11250 / Sci species name: Human respiratory syncytial virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: ribonucleocapsid
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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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: HBSS, 25 mM Hepes
GridDetails: C-flat 2/2-2C and C-flat 2/2-4C, 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
DateJul 11, 2012
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

DetailsSubtomograms were manually selected from the tomograms by visual inspection
Final reconstructionResolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, PEET, Bsoft / Number subtomograms used: 1402

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