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- EMDB-20584: A potent cross-neutralizing antibody targeting the fusion glycopr... -

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Basic information

Entry
Database: EMDB / ID: EMD-20584
TitleA potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah virus and Hendra virus infection
Map data
SampleNipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment:
(Fusion glycoprotein ...) x 2 / 5B3 antibody / (5B3 antibody ...) x 2 / (ligand) x 3
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / membrane fusion involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / integral component of membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesNipah virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDang HV / Chan YP / Park YJ / Snijder J / Da Silva SC / Vu B / Yan L / Feng YR / Rockx B / Geisbert T / Mire CE / Broder CB / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences120553 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections.
Authors: Ha V Dang / Yee-Peng Chan / Young-Jun Park / Joost Snijder / Sofia Cheliout Da Silva / Bang Vu / Lianying Yan / Yan-Ru Feng / Barry Rockx / Thomas W Geisbert / Chad E Mire / 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 with fatality rates of 50-100%. No vaccines or licensed ...Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness with fatality rates of 50-100%. No vaccines or licensed therapeutics currently exist to protect humans against NiV or HeV. HNVs enter host cells by fusing the viral and cellular membranes via the concerted action of the attachment (G) and fusion (F) glycoproteins, the main targets of the humoral immune response. Here, we describe the isolation and humanization of a potent monoclonal antibody cross-neutralizing NiV and HeV. Cryo-electron microscopy, triggering and fusion studies show the antibody binds to a prefusion-specific quaternary epitope, conserved in NiV F and HeV F glycoproteins, and prevents membrane fusion and viral entry. This work supports the importance of the HNV prefusion F conformation for eliciting a robust immune response and paves the way for using this antibody for prophylaxis and post-exposure therapy with NiV- and HeV-infected individuals.
Validation ReportPDB-ID: 6tys

SummaryFull reportAbout validation report
History
DepositionAug 9, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6tys
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6tys
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20584.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 256 pix.
= 350.72 Å
1.37 Å/pix.
x 256 pix.
= 350.72 Å
1.37 Å/pix.
x 256 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-0.6020366 - 1.7019674
Average (Standard dev.)0.002559473 (±0.05926141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 350.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z350.720350.720350.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.9754.6820.005

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Supplemental data

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Sample components

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Entire Nipah virus fusion (F) glycoprotein in complex with the 5B3 antib...

EntireName: Nipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment
Number of components: 9

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Component #1: protein, Nipah virus fusion (F) glycoprotein in complex with the ...

ProteinName: Nipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment
Recombinant expression: No

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Component #2: protein, Fusion glycoprotein F0

ProteinName: Fusion glycoprotein F0 / Recombinant expression: No
SourceSpecies: Nipah virus
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, 5B3 antibody

ProteinName: 5B3 antibody / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #4: protein, Fusion glycoprotein F0

ProteinName: Fusion glycoprotein F0 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 59.704781 kDa
SourceSpecies: Nipah virus
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, 5B3 antibody heavy chain

ProteinName: 5B3 antibody heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.245752 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #6: protein, 5B3 antibody light chain

ProteinName: 5B3 antibody light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.517844 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #8: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 38721
3D reconstructionSoftware: cryoSPARC / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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