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- EMDB-42987: Structure of the Human Respirovirus 3 Fusion Protein Bound to Cam... -

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Basic information

Entry
Database: EMDB / ID: EMD-42987
TitleStructure of the Human Respirovirus 3 Fusion Protein Bound to Camelid Nanobodies 1D10 and 4C06
Map dataFinal refined volume. DeepEMhancer sharpened. Used to build coordinates.
Sample
  • Complex: Prefusion Human Respirovirus 3 Fusion Protein Bound to Camelid Nanobodies 1D10 and 4C06
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Camelid nanobody 1D10
    • Protein or peptide: Camelid nanobody 4C06
Keywordsviral fusion protein / camelid nanobodies / 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 / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman respirovirus 3 / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJohnson NJ / Ramamohan AR / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for potent neutralization of human respirovirus type 3 by protective single-domain camelid antibodies.
Authors: Nicole V Johnson / Revina C van Scherpenzeel / Mark J G Bakkers / Ajit R Ramamohan / Daan van Overveld / Lam Le / Johannes P M Langedijk / Joost A Kolkman / Jason S McLellan /
Abstract: Respirovirus 3 is a leading cause of severe acute respiratory infections in vulnerable human populations. Entry into host cells is facilitated by the attachment glycoprotein and the fusion ...Respirovirus 3 is a leading cause of severe acute respiratory infections in vulnerable human populations. Entry into host cells is facilitated by the attachment glycoprotein and the fusion glycoprotein (F). Because of its crucial role, F represents an attractive therapeutic target. Here, we identify 13 F-directed heavy-chain-only antibody fragments that neutralize recombinant respirovirus 3. High-resolution cryo-EM structures of antibody fragments bound to the prefusion conformation of F reveal three distinct, previously uncharacterized epitopes. All three antibody fragments bind quaternary epitopes on F, suggesting mechanisms for neutralization that may include stabilization of the prefusion conformation. Studies in cotton rats demonstrate the prophylactic efficacy of these antibody fragments in reducing viral load in the lungs and nasal passages. These data highlight the potential of heavy-chain-only antibody fragments as effective interventions against respirovirus 3 infection and identify neutralizing epitopes that can be targeted for therapeutic development.
History
DepositionDec 1, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42987.png

Downloads & links

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Map

FileDownload / File: emd_42987.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal refined volume. DeepEMhancer sharpened. Used to build coordinates.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.03330007 - 1.9704101
Average (Standard dev.)0.0011425883 (±0.02531491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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

Fileemd_42987_additional_1.map
AnnotationFinal refined 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_42987_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_42987_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 : Prefusion Human Respirovirus 3 Fusion Protein Bound to Camelid Na...

EntireName: Prefusion Human Respirovirus 3 Fusion Protein Bound to Camelid Nanobodies 1D10 and 4C06
Components
  • Complex: Prefusion Human Respirovirus 3 Fusion Protein Bound to Camelid Nanobodies 1D10 and 4C06
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Camelid nanobody 1D10
    • Protein or peptide: Camelid nanobody 4C06

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Supramolecule #1: Prefusion Human Respirovirus 3 Fusion Protein Bound to Camelid Na...

SupramoleculeName: Prefusion Human Respirovirus 3 Fusion Protein Bound to Camelid Nanobodies 1D10 and 4C06
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 277.5 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: 57.336508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPISILLIIT TMIMASHCQI DITKLQHVGV LVNSPKGMKI SQNFETRYLI LSLIPKIEDS NSCGDQQIKQ YKRLLDRLII PLYDGLRLQ KDVIVTNQES NENTDPRTER FFGGVIGTIA LGVATSAQIT AAVALVEAKQ ARSDIEKLKE AIRDTNKAVQ S VQSSPGNL ...String:
MPISILLIIT TMIMASHCQI DITKLQHVGV LVNSPKGMKI SQNFETRYLI LSLIPKIEDS NSCGDQQIKQ YKRLLDRLII PLYDGLRLQ KDVIVTNQES NENTDPRTER FFGGVIGTIA LGVATSAQIT AAVALVEAKQ ARSDIEKLKE AIRDTNKAVQ S VQSSPGNL IVAIKSVQDY VNKEIVPCIA RLGCEACGLL LGLALDQHYS ELTNIFGDNI GSLQEKGIKL QGIASLYRTN IT EIFTTST VDKYDIYDLL FTESIKVRVI DVDLNDYSIT LQVRLPLLTR LLNTQIYKVD SISYNIQNRE WYIPLPSHIM TKG AFLGGA DVKECIEAFS SYICPSDPGF VLNHEMESCL SGNISQCPRT TVTSDIVPRY AFVNGGVVAN CITTTCTCNG IGNR INQPP DQGVKIITHK ECNTIGINGM LFNTNKEGTL AFYTPDDITL NNSVALNPID ISIELNKAKS DLEESKEWIR RSNQK LDSI EDKIEEILSK IYHIENEIAR IKKLIGEAEP EA

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Camelid nanobody 1D10

MacromoleculeName: Camelid nanobody 1D10 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.436922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQTGDSLRL SCAASGSIFG ENAMAWFRQA PGKQRELVAR VSTGGTLFYA DFAKVRFTIS RDTAKQTVYL QMSSLRPED TAVYYCAVAV GTRNYWGQGT QVTVSS

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Macromolecule #3: Camelid nanobody 4C06

MacromoleculeName: Camelid nanobody 4C06 / type: protein_or_peptide / ID: 3 / 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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56650
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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