+Open data
-Basic information
Entry | Database: PDB / ID: 8dnr | ||||||
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Title | Prefusion-stabilized Hendra virus fusion protein | ||||||
Components | Fusion glycoprotein F0 | ||||||
Keywords | VIRAL PROTEIN / Hendra / nipah / henipavirus / Hendra virus / NiV / HeV / fusion / F / antibody / neutralizing / conserved epitope / neutralizing antibody / prefusion / prefusion-stabilized / vaccine / vaccine design / antigen / antigen design | ||||||
Function / homology | Function and homology information host cell surface / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Hendra henipavirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Byrne, P.O. / Blade, E.G. / McLellan, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Virol / Year: 2024 Title: Prefusion stabilization of the Hendra and Langya virus F proteins. Authors: Patrick O Byrne / Elizabeth G Blade / Brian E Fisher / David R Ambrozak / Ajit R Ramamohan / Barney S Graham / Rebecca J Loomis / Jason S McLellan / Abstract: Nipah virus (NiV) and Hendra virus (HeV) are pathogenic paramyxoviruses that cause mild-to-severe disease in humans. As members of the genus, NiV and HeV use an attachment (G) glycoprotein and a ...Nipah virus (NiV) and Hendra virus (HeV) are pathogenic paramyxoviruses that cause mild-to-severe disease in humans. As members of the genus, NiV and HeV use an attachment (G) glycoprotein and a class I fusion (F) glycoprotein to invade host cells. The F protein rearranges from a metastable prefusion form to an extended postfusion form to facilitate host cell entry. Prefusion NiV F elicits higher neutralizing antibody titers than postfusion NiV F, indicating that stabilization of prefusion F may aid vaccine development. A combination of amino acid substitutions (L104C/I114C, L172F, and S191P) is known to stabilize NiV F in its prefusion conformation, although the extent to which substitutions transfer to other henipavirus F proteins is not known. Here, we perform biophysical and structural studies to investigate the mechanism of prefusion stabilization in F proteins from three henipaviruses: NiV, HeV, and Langya virus (LayV). Three known stabilizing substitutions from NiV F transfer to HeV F and exert similar structural and functional effects. One engineered disulfide bond, located near the fusion peptide, is sufficient to stabilize the prefusion conformations of both HeV F and LayV F. Although LayV F shares low overall sequence identity with NiV F and HeV F, the region around the fusion peptide exhibits high sequence conservation across all henipaviruses. Our findings indicate that substitutions targeting this site of conformational change might be applicable to prefusion stabilization of other henipavirus F proteins and support the use of NiV as a prototypical pathogen for henipavirus vaccine antigen design.IMPORTANCEPathogenic henipaviruses such as Nipah virus (NiV) and Hendra virus (HeV) cause respiratory symptoms, with severe cases resulting in encephalitis, seizures, and coma. The work described here shows that the NiV and HeV fusion (F) proteins share common structural features with the F protein from an emerging henipavirus Langya virus (LayV). Sequence alignment alone was sufficient to predict which known prefusion-stabilizing amino acid substitutions from NiV F would stabilize the prefusion conformations of HeV F and LayV F. This work also reveals an unexpected oligomeric interface shared by prefusion HeV F and NiV F. Together, these advances lay a foundation for future antigen design targeting henipavirus F proteins. In this way, Nipah virus can serve as a prototypical pathogen for the development of protective vaccines and monoclonal antibodies to prepare for potential henipavirus outbreaks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dnr.cif.gz | 254.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dnr.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dnr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8dnr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8dnr_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 8dnr_validation.cif.gz | 73.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/8dnr ftp://data.pdbj.org/pub/pdb/validation_reports/dn/8dnr | HTTPS FTP |
-Related structure data
Related structure data | 27577MC 8dngC 8do4C 8u1rC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 48721.742 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hendra henipavirus / Strain: isolate Horse/Autralia/Hendra/1994 / Production host: Homo sapiens (human) / References: UniProt: O89342 #2: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Prefusion-stabilized Hendra virus fusion protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Hendra henipavirus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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Image processing | Details: Prefusion-stabilized Hendra virus fusion protein. homotrimer |
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114178 / Symmetry type: POINT |