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- EMDB-27550: Subtomogram average of the HN/F fusion complex on authentic viral... -

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Basic information

Entry
Database: EMDB / ID: EMD-27550
TitleSubtomogram average of the HN/F fusion complex on authentic viral surfaces of HPIV3
Map dataCombined HN and F EM map after focused refinement
Sample
  • Virus: Human respirovirus 3
Biological speciesHuman respirovirus 3
Methodsubtomogram averaging / cryo EM / Resolution: 10.2 Å
AuthorsMarcink TC / Porotto M / des Georges A / Moscona A
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI152275 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI121349 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI160953 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI160961 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI114736 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133598 United States
CitationJournal: Sci Adv / Year: 2023
Title: Subnanometer structure of an enveloped virus fusion complex on viral surface reveals new entry mechanisms.
Authors: Tara C Marcink / Gillian Zipursky / Wenjing Cheng / Kyle Stearns / Shari Stenglein / Kate Golub / Frances Cohen / Francesca Bovier / Daniel Pfalmer / Alexander L Greninger / Matteo Porotto / ...Authors: Tara C Marcink / Gillian Zipursky / Wenjing Cheng / Kyle Stearns / Shari Stenglein / Kate Golub / Frances Cohen / Francesca Bovier / Daniel Pfalmer / Alexander L Greninger / Matteo Porotto / Amedee des Georges / Anne Moscona /
Abstract: Paramyxoviruses-including important pathogens like parainfluenza, measles, and Nipah viruses-use a receptor binding protein [hemagglutinin-neuraminidase (HN) for parainfluenza] and a fusion protein ...Paramyxoviruses-including important pathogens like parainfluenza, measles, and Nipah viruses-use a receptor binding protein [hemagglutinin-neuraminidase (HN) for parainfluenza] and a fusion protein (F), acting in a complex, to enter cells. We use cryo-electron tomography to visualize the fusion complex of human parainfluenza virus 3 (HN/F) on the surface of authentic clinical viruses at a subnanometer resolution sufficient to answer mechanistic questions. An HN loop inserts in a pocket on F, showing how the fusion complex remains in a ready but quiescent state until activation. The globular HN heads are rotated with respect to each other: one downward to contact F, and the other upward to grapple cellular receptors, demonstrating how HN/F performs distinct steps before F activation. This depiction of viral fusion illuminates potentially druggable targets for paramyxoviruses and sheds light on fusion processes that underpin wide-ranging biological processes but have not been visualized in situ or at the present resolution.
History
DepositionJul 10, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27550.png

Downloads & links

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Map

FileDownload / File: emd_27550.map.gz / Format: CCP4 / Size: 23.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined HN and F EM map after focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 184 pix.
= 316.48 Å		1.72 Å/pix.
x 184 pix.
= 316.48 Å		1.72 Å/pix.
x 184 pix.
= 316.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-40.343395 - 21.971916
Average (Standard dev.)-0.52784276 (±0.7990761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions184184184
Spacing184184184
CellA=B=C: 316.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: F-focused refinement EM map

Fileemd_27550_additional_1.map
AnnotationF-focused refinement EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: HN-focused refinement EM map

Fileemd_27550_additional_2.map
AnnotationHN-focused refinement EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: HN and F EM map before focused refinement

Fileemd_27550_additional_3.map
AnnotationHN and F EM map before focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human respirovirus 3

EntireName: Human respirovirus 3
Components
  • Virus: Human respirovirus 3

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Supramolecule #1: Human respirovirus 3

SupramoleculeName: Human respirovirus 3 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11216 / Sci species name: Human respirovirus 3 / 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 stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0035 µm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 11845
ExtractionNumber tomograms: 11 / Number images used: 24976
Final angle assignmentType: ANGULAR RECONSTITUTION

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