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Yorodumi- EMDB-26164: Nipah Virus attachment (G) glycoprotein ectodomain in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26164 | |||||||||
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Title | Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (global refinement) | |||||||||
Map data | ||||||||||
Sample |
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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 / metal ion binding Similarity search - Function | |||||||||
Biological species | Nipah henipavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Wang ZQ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D | |||||||||
Funding support | United States, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_26164.map.gz | 350.9 MB | EMDB map data format | |
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Header (meta data) | emd-26164-v30.xml emd-26164.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_26164.png | 80.4 KB | ||
Others | emd_26164_additional_1.map.gz emd_26164_half_map_1.map.gz emd_26164_half_map_2.map.gz | 186.4 MB 344.1 MB 344.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26164 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26164 | HTTPS FTP |
-Validation report
Summary document | emd_26164_validation.pdf.gz | 493.8 KB | Display | EMDB validaton report |
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Full document | emd_26164_full_validation.pdf.gz | 493.4 KB | Display | |
Data in XML | emd_26164_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_26164_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26164 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26164 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26164.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_26164_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26164_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26164_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nipah Virus attachment protein ectodomain in complex with nAH1.3 ...
Entire | Name: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment |
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Components |
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-Supramolecule #1: Nipah Virus attachment protein ectodomain in complex with nAH1.3 ...
Supramolecule | Name: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Nipah henipavirus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168035 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |