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- EMDB-26164: Nipah Virus attachment (G) glycoprotein ectodomain in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-26164
TitleNipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (global refinement)
Map data
Sample
  • Complex: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding ...membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular exosome / identical protein binding / membrane / metal ion binding
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Igh protein / Glycoprotein G
Similarity search - Component
Biological speciesNipah henipavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang ZQ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: 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
DepositionFeb 10, 2022-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_26164.png

Downloads & links

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Map

FileDownload / File: emd_26164.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.955034 - 3.3588252
Average (Standard dev.)-0.00042927897 (±0.045748666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 482.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z483.000483.000483.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-1.9553.359-0.000

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Supplemental data

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Additional map: #1

Fileemd_26164_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_26164_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26164_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Nipah Virus attachment protein ectodomain in complex with nAH1.3 ...

EntireName: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment
Components
  • Complex: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment

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Supramolecule #1: Nipah Virus attachment protein ectodomain in complex with nAH1.3 ...

SupramoleculeName: 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
Source (natural)Organism: Nipah henipavirus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3d11

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168035
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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