+Open data
-Basic information
Entry | Database: PDB / ID: 8fmy | ||||||
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Title | Mojiang virus F ectodomain in prefusion form | ||||||
Components | Fusion glycoprotein F0 | ||||||
Keywords | VIRAL PROTEIN / F ectodomain / prefusion | ||||||
Function / homology | Precursor 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 species | Mojiang virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å | ||||||
Authors | Low, Y.S. / Isaacs, A. / Modhiran, N. / Watterson, D. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure and antigenicity of divergent Henipavirus fusion glycoproteins. Authors: Ariel Isaacs / Yu Shang Low / Kyle L Macauslane / Joy Seitanidou / Cassandra L Pegg / Stacey T M Cheung / Benjamin Liang / Connor A P Scott / Michael J Landsberg / Benjamin L Schulz / Keith ...Authors: Ariel Isaacs / Yu Shang Low / Kyle L Macauslane / Joy Seitanidou / Cassandra L Pegg / Stacey T M Cheung / Benjamin Liang / Connor A P Scott / Michael J Landsberg / Benjamin L Schulz / Keith J Chappell / Naphak Modhiran / Daniel Watterson / Abstract: In August 2022, a novel henipavirus (HNV) named Langya virus (LayV) was isolated from patients with severe pneumonic disease in China. This virus is closely related to Mòjiāng virus (MojV), and ...In August 2022, a novel henipavirus (HNV) named Langya virus (LayV) was isolated from patients with severe pneumonic disease in China. This virus is closely related to Mòjiāng virus (MojV), and both are divergent from the bat-borne HNV members, Nipah (NiV) and Hendra (HeV) viruses. The spillover of LayV is the first instance of a HNV zoonosis to humans outside of NiV and HeV, highlighting the continuing threat this genus poses to human health. In this work, we determine the prefusion structures of MojV and LayV F proteins via cryogenic electron microscopy to 2.66 and 3.37 Å, respectively. We show that despite sequence divergence from NiV, the F proteins adopt an overall similar structure but are antigenically distinct as they do not react to known antibodies or sera. Glycoproteomic analysis revealed that while LayV F is less glycosylated than NiV F, it contains a glycan that shields a site of vulnerability previously identified for NiV. These findings explain the distinct antigenic profile of LayV and MojV F, despite the extent to which they are otherwise structurally similar to NiV. Our results carry implications for broad-spectrum HNV vaccines and therapeutics, and indicate an antigenic, yet not structural, divergence from prototypical HNVs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fmy.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fmy.ent.gz | 174.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fmy_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8fmy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8fmy_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 8fmy_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/8fmy ftp://data.pdbj.org/pub/pdb/validation_reports/fm/8fmy | HTTPS FTP |
-Related structure data
Related structure data | 29300MC 8fmxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 26 - 445 / Label seq-ID: 26 - 445
NCS oper:
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-Components
#1: Protein | Mass: 52636.922 Da / Num. of mol.: 3 / Fragment: ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mojiang virus / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: W8SKT3 |
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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: Mojiang virus F glycoprotein ectodomain in the prefusion form Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.2 MDa / Experimental value: NO |
Source (natural) | Organism: Mojiang virus |
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) |
Buffer solution | pH: 6.8 |
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.255% CHAPS added |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2543223 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213754 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 102.7 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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