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Yorodumi- PDB-7txz: Nipah Virus attachment (G) glycoprotein ectodomain in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7txz | ||||||
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Title | Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (local refinement of the distal region) | ||||||
Components |
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Keywords | VIRAL PROTEIN / NiV / NiVG / attachment protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Nipah henipavirus Mus sp. (mice) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Wang, Z.Q. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2022 Title: Architecture and antigenicity of the Nipah virus attachment glycoprotein. Authors: Zhaoqian Wang / Moushimi Amaya / Amin Addetia / Ha V Dang / Gabriella Reggiano / Lianying Yan / Andrew C Hickey / Frank DiMaio / Christopher C Broder / David Veesler / Abstract: Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness. The entry of HNVs into host cells requires the attachment ...Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness. The entry of HNVs into host cells requires the attachment (G) and fusion (F) glycoproteins, which are the main targets of antibody responses. To understand viral infection and host immunity, we determined a cryo-electron microscopy structure of the NiV G homotetrameric ectodomain in complex with the nAH1.3 broadly neutralizing antibody Fab fragment. We show that a cocktail of two nonoverlapping G-specific antibodies neutralizes NiV and HeV synergistically and limits the emergence of escape mutants. Analysis of polyclonal serum antibody responses elicited by vaccination of macaques with NiV G indicates that the receptor binding head domain is immunodominant. These results pave the way for implementing multipronged therapeutic strategies against these deadly pathogens. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7txz.cif.gz | 321.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7txz.ent.gz | 238.2 KB | Display | PDB format |
PDBx/mmJSON format | 7txz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7txz_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7txz_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7txz_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 7txz_validation.cif.gz | 79.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7txz ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txz | HTTPS FTP |
-Related structure data
Related structure data | 26162MC 7ty0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 4 molecules ABDC
#1: Protein | Mass: 60358.535 Da / Num. of mol.: 4 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nipah henipavirus / Production host: Homo sapiens (human) / References: UniProt: Q9IH62 |
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-Antibody , 2 types, 4 molecules EHFL
#2: Antibody | Mass: 50643.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus sp. (mice) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23947.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus sp. (mice) / Production host: Homo sapiens (human) |
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-Sugars , 3 types, 14 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 70 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168035 / Symmetry type: POINT |