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- EMDB-42981: Prefusion-stabilized Respirovirus type 3 Fusion protein -

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Basic information

Entry
Database: EMDB / ID: EMD-42981
TitlePrefusion-stabilized Respirovirus type 3 Fusion protein
Map dataFinal refinement volume. DeepEMhancer sharpened. Used to build coordinates.
Sample
  • Complex: Trimeric Human Respirovirus 3 Fusion Protein bound to 3 copies of nanobody 4C06
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Camelid nanobody 4C06
Keywordsfusion protein / viral glycoprotein / membrane fusion / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman respirovirus 3 / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJohnson NV / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Universal paramyxovirus vaccine design by stabilizing regions involved in structural transformation of the fusion protein.
Authors: Johannes P M Langedijk / Freek Cox / Nicole V Johnson / Daan van Overveld / Lam Le / Ward van den Hoogen / Richard Voorzaat / Roland Zahn / Leslie van der Fits / Jarek Juraszek / Jason S ...Authors: Johannes P M Langedijk / Freek Cox / Nicole V Johnson / Daan van Overveld / Lam Le / Ward van den Hoogen / Richard Voorzaat / Roland Zahn / Leslie van der Fits / Jarek Juraszek / Jason S McLellan / Mark J G Bakkers /
Abstract: The Paramyxoviridae family encompasses medically significant RNA viruses, including human respiroviruses 1 and 3 (RV1, RV3), and zoonotic pathogens like Nipah virus (NiV). RV3, previously known as ...The Paramyxoviridae family encompasses medically significant RNA viruses, including human respiroviruses 1 and 3 (RV1, RV3), and zoonotic pathogens like Nipah virus (NiV). RV3, previously known as parainfluenza type 3, for which no vaccines or antivirals have been approved, causes respiratory tract infections in vulnerable populations. The RV3 fusion (F) protein is inherently metastable and will likely require prefusion (preF) stabilization for vaccine effectiveness. Here we used structure-based design to stabilize regions involved in structural transformation to generate a preF protein vaccine antigen with high expression and stability, and which, by stabilizing the coiled-coil stem region, does not require a heterologous trimerization domain. The preF candidate induces strong neutralizing antibody responses in both female naïve and pre-exposed mice and provides protection in a cotton rat challenge model (female). Despite the evolutionary distance of paramyxovirus F proteins, their structural transformation and local regions of instability are conserved, which allows successful transfer of stabilizing substitutions to the distant preF proteins of RV1 and NiV. This work presents a successful vaccine antigen design for RV3 and provides a toolbox for future paramyxovirus vaccine design and pandemic preparedness.
History
DepositionNov 30, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42981.png

Downloads & links

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Map

FileDownload / File: emd_42981.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal refinement volume. DeepEMhancer sharpened. Used to build coordinates.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.024504988 - 1.5457215
Average (Standard dev.)0.00072672433 (±0.01850146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 311.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Final refinement volume. Sharpened map, not DeepEMhancer sharpened.

Fileemd_42981_additional_1.map
AnnotationFinal refinement volume. Sharpened map, not DeepEMhancer sharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_42981_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_42981_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric Human Respirovirus 3 Fusion Protein bound to 3 copies of...

EntireName: Trimeric Human Respirovirus 3 Fusion Protein bound to 3 copies of nanobody 4C06
Components
  • Complex: Trimeric Human Respirovirus 3 Fusion Protein bound to 3 copies of nanobody 4C06
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Camelid nanobody 4C06

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Supramolecule #1: Trimeric Human Respirovirus 3 Fusion Protein bound to 3 copies of...

SupramoleculeName: Trimeric Human Respirovirus 3 Fusion Protein bound to 3 copies of nanobody 4C06
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 232.5 KDa

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 54.147891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPISILLIIT TMIMASHCQI DITKLQHVGV LVNSPKGMKI PQNFETRYLI LSLIPKIEDS NSCGDQQIKQ YKRLLDRLII PLYDGLRLM KDVIVTNQES NENTDPRTER FFGGVIGTIA LGVATSAQIT AAVALVEAKQ ARSDIEKLKE AIRDTNKAVQ S VQSSVGPP ...String:
MPISILLIIT TMIMASHCQI DITKLQHVGV LVNSPKGMKI PQNFETRYLI LSLIPKIEDS NSCGDQQIKQ YKRLLDRLII PLYDGLRLM KDVIVTNQES NENTDPRTER FFGGVIGTIA LGVATSAQIT AAVALVEAKQ ARSDIEKLKE AIRDTNKAVQ S VQSSVGPP IVAIKSVQDY VNKEIVPSIA RLGCEAAGLQ LGIALTQHYS ELTNIFGDNI GSLIEKGIKL QGIASLYRTN IT EIFTTST VDKYDIYDLL FTESIKVRVI DVDLNDYSIT LQVRLPLLTR LLNTQIYKVD SISYNIQNRE WYIPLPSHIM TKG AFLGGA DVKECIEAPS SYICPSDPGF VLNHEMESCL SGNISQCPRT TVTSDIVPRY AFVNGGVVAN CITTTCTCNG IGNR INQPP DQGVKIITHK ECNTIGINGM LFNTNKEGTL AFYTPDDITL NNSVALNPID ISIELNKAKS DLEEVKEWIR RVNQK LDSI GSGEPEA

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Camelid nanobody 4C06

MacromoleculeName: Camelid nanobody 4C06 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.487816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCSASGSLST IKALGWYRRA PGRERELVAS ITSAGETNYA DSAKGRFTVS TDNAKNTVDL RMNSLKPED TAVYYCYAES FVLNIYWGQG TQVTVSSG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6mjz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193265
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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