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- EMDB-2393: Electron cryomicroscopy of human Respiratory Syncytial Virus post... -

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Basic information

Entry
Database: EMDB / ID: EMD-2393
TitleElectron cryomicroscopy of human Respiratory Syncytial Virus postfusion F
Map dataSubtomogram average of hRSV postfusion F
Sample
  • Sample: Human Respiratory Syncytial Virus
  • Protein or peptide: prefusion F
KeywordsRSV / fusion protein / postfusion
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Methodsubtomogram averaging / cryo EM / Resolution: 36.0 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: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2393.tif

Downloads & links

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Map

FileDownload / File: emd_2393.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of hRSV postfusion F
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.68 Å/pix.
x 112 pix.
= 860.16 Å		7.68 Å/pix.
x 112 pix.
= 860.16 Å		7.68 Å/pix.
x 112 pix.
= 860.16 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 EMDB: 2.0 / Movie #1: 4
Minimum - Maximum-12.705457689999999 - 36.983715060000002
Average (Standard dev.)-0.00000021 (±0.99999613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 860.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.687.687.68
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z860.160860.160860.160
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
D min/max/mean-12.70536.984-0.000

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Supplemental data

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Sample components

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Entire : Human Respiratory Syncytial Virus

EntireName: Human Respiratory Syncytial Virus
Components
  • Sample: Human Respiratory Syncytial Virus
  • Protein or peptide: prefusion F

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Supramolecule #1000: Human Respiratory Syncytial Virus

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

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Macromolecule #1: prefusion F

MacromoleculeName: prefusion F / type: protein_or_peptide / ID: 1 / Oligomeric state: Trimer / Recombinant expression: No
Source (natural)Organism: Human respiratory syncytial virus
SequenceUniProtKB: Fusion glycoprotein F0

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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
DateOct 28, 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: 5.0 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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, PEET, Bsoft / Number subtomograms used: 2857

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Atomic model buiding 1

Initial modelPDB ID:

3rrt

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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