+Open data
-Basic information
Entry | Database: PDB / ID: 8k3c | ||||||
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Title | Nipah virus Attachment glycoprotein with 41-6 antibody fragment | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Nipah virus / Attachment glycoprotein / tetramer complex / Neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Henipavirus nipahense | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å | ||||||
Authors | Sun, M.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Potent human neutralizing antibodies against Nipah virus derived from two ancestral antibody heavy chains. Authors: Li Chen / Mengmeng Sun / Huajun Zhang / Xinghai Zhang / Yanfeng Yao / Ming Li / Kangyin Li / Pengfei Fan / Haiwei Zhang / Ye Qin / Zhe Zhang / Entao Li / Zhen Chen / Wuxiang Guan / Shanshan ...Authors: Li Chen / Mengmeng Sun / Huajun Zhang / Xinghai Zhang / Yanfeng Yao / Ming Li / Kangyin Li / Pengfei Fan / Haiwei Zhang / Ye Qin / Zhe Zhang / Entao Li / Zhen Chen / Wuxiang Guan / Shanshan Li / Changming Yu / Kaiming Zhang / Rui Gong / Sandra Chiu / Abstract: Nipah virus (NiV) is a World Health Organization priority pathogen and there are currently no approved drugs for clinical immunotherapy. Through the use of a naïve human phage-displayed Fab library, ...Nipah virus (NiV) is a World Health Organization priority pathogen and there are currently no approved drugs for clinical immunotherapy. Through the use of a naïve human phage-displayed Fab library, two neutralizing antibodies (NiV41 and NiV42) targeting the NiV receptor binding protein (RBP) were identified. Following affinity maturation, antibodies derived from NiV41 display cross-reactivity against both NiV and Hendra virus (HeV), whereas the antibody based on NiV42 is only specific to NiV. Results of immunogenetic analysis reveal a correlation between the maturation of antibodies and their antiviral activity. In vivo testing of NiV41 and its mature form (41-6) show protective efficacy against a lethal NiV challenge in hamsters. Furthermore, a 2.88 Å Cryo-EM structure of the tetrameric RBP and antibody complex demonstrates that 41-6 blocks the receptor binding interface. These findings can be beneficial for the development of antiviral drugs and the design of vaccines with broad spectrum against henipaviruses. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k3c.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k3c.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 8k3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/8k3c ftp://data.pdbj.org/pub/pdb/validation_reports/k3/8k3c | HTTPS FTP |
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-Related structure data
Related structure data | 36849MC 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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1 |
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-Components
#1: Antibody | Mass: 22844.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 |
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#2: Antibody | Mass: 25312.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 |
#3: Protein | Mass: 52941.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Henipavirus nipahense / Cell line (production host): Expi293F cells / Production host: Homo sapiens (human) / References: UniProt: Q9IH62 |
-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: Cryo-EM structure of complex of attachment glycoprotein G with 41-6 Fab fragment Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||
Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 3 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9103 |
Image scans | Width: 4092 / Height: 5760 |
-Processing
CTF correction | Type: NONE |
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Particle selection | Num. of particles selected: 879898 |
3D reconstruction | Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299497 / Symmetry type: POINT |