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- EMDB-43914: Subtomogram average of the HN-F complex on the viral surface of a... -

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Entry
Database: EMDB / ID: EMD-43914
TitleSubtomogram average of the HN-F complex on the viral surface of an HPIV3 escape variant (EV1).
Map dataSubtomogram average of the HN-F complex on the viral surface of an HPIV3 escape variant (EV1)
Sample
  • Virus: Human respirovirus 3
Keywordsvirus / glycoproteins / fusion protein / Hemagglutinin-neuraminidase / viral evolution / tomography / fusion complex / HPIV3 / paraflu / VIRAL PROTEIN
Biological speciesHuman respirovirus 3
Methodsubtomogram averaging / cryo EM / Resolution: 12.2 Å
AuthorsMarcink TC / Moscona A
Funding support United States, 5 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)AI114736 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI160961 United States
CitationJournal: Nat Commun / Year: 2024
Title: How a paramyxovirus fusion/entry complex adapts to escape a neutralizing antibody.
Authors: Tara C Marcink / Gillian Zipursky / Elizabeth B Sobolik / Kate Golub / Emily Herman / Kyle Stearns / Alexander L Greninger / Matteo Porotto / Anne Moscona /
Abstract: Paramyxoviruses including measles, Nipah, and parainfluenza viruses are public health threats with pandemic potential. Human parainfluenza virus type 3 (HPIV3) is a leading cause of illness in ...Paramyxoviruses including measles, Nipah, and parainfluenza viruses are public health threats with pandemic potential. Human parainfluenza virus type 3 (HPIV3) is a leading cause of illness in pediatric, older, and immunocompromised populations. There are no approved vaccines or therapeutics for HPIV3. Neutralizing monoclonal antibodies (mAbs) that target viral fusion are a potential strategy for mitigating paramyxovirus infection, however their utility may be curtailed by viral evolution that leads to resistance. Paramyxoviruses enter cells by fusing with the cell membrane in a process mediated by a complex consisting of a receptor binding protein (HN) and a fusion protein (F). Existing atomic resolution structures fail to reveal physiologically relevant interactions during viral entry. We present cryo-ET structures of pre-fusion HN-F complexes in situ on surfaces of virions that evolved resistance to an anti-HPIV3 F neutralizing mAb. Single mutations in F abolish mAb binding and neutralization. In these complexes, the HN protein that normally restrains F triggering has shifted to uncap the F apex. These complexes are more readily triggered to fuse. These structures shed light on the adaptability of the pre-fusion HN-F complex and mechanisms of paramyxoviral resistance to mAbs, and help define potential barriers to resistance for the design of mAbs.
History
DepositionMar 4, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43914.png

Downloads & links

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Map

FileDownload / File: emd_43914.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the HN-F complex on the viral surface of an HPIV3 escape variant (EV1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 128 pix.
= 438.016 Å		3.42 Å/pix.
x 128 pix.
= 438.016 Å		3.42 Å/pix.
x 128 pix.
= 438.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.288
Minimum - Maximum-0.63072956 - 1.4965686
Average (Standard dev.)0.018684383 (±0.065313004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 438.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_43914_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_43914_half_map_2.map
AnnotationHalf Map A
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 statecell

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Sample preparation

BufferpH: 7.4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 3.5 µm

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 5269
ExtractionNumber tomograms: 12 / Number images used: 5269
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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