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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 dataSharpened map
Sample
  • Complex: Nipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment
    • Complex: Fusion glycoprotein F0
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5B3 antibody
      • Protein or peptide: 5B3 antibody heavy chain
      • Protein or peptide: 5B3 antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHenipavirus / Nipah virus / Hendra virus / fusion glycoprotein / antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesNipah virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDang HV / Chan YP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)120553 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 ...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.
History
DepositionAug 9, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing 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 modelsPDB-6tys
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20584.png

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)
AnnotationSharpened map
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-2.974538 - 4.6816626
Average (Standard dev.)0.005286577 (±0.09749216)
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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Additional map: Unsharpened map

Fileemd_20584_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Components
  • Complex: Nipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment
    • Complex: Fusion glycoprotein F0
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5B3 antibody
      • Protein or peptide: 5B3 antibody heavy chain
      • Protein or peptide: 5B3 antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Nipah virus fusion (F) glycoprotein in complex with the 5B3 antib...

SupramoleculeName: Nipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Fusion glycoprotein F0

SupramoleculeName: Fusion glycoprotein F0 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Nipah virus

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Supramolecule #3: 5B3 antibody

SupramoleculeName: 5B3 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nipah virus
Molecular weightTheoretical: 59.704781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN CTHDLDYKDD DDKVGDVRLA GVIMAGVCIG IATAAQITAG VALYEAMKNA DNINKLKSSI E STNEAVVK ...String:
MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN CTHDLDYKDD DDKVGDVRLA GVIMAGVCIG IATAAQITAG VALYEAMKNA DNINKLKSSI E STNEAVVK LQETAEKTVY VLTALQDYIN TNLVPTIDKI SCKQTELSLD LALSKYLSDL LFVFGPNLQD PVSNSMTIQA IS QAFGGNY ETLLRTLGYA TEDFDDLLES DSITGQIIYV DLSSYYIIVR VYFPILTEIQ QAYIQELLPV SFNNDNSEWI SIV PNFILV RNTLISNIEI GFCLITKRSV ICNQDYATPM TNNMRECLTG STEKCPRELV VSSHVPRFAL SNGVLFANCI SVTC QCQTT GRAISQSGEQ TLLMIDNTTC PTAVLGNVII SLGKYLGSVN YNSEGIAIGP PVFTDKVDIS SQISSMNQSL QQSKD YIKE AQRLLDTVNP SLISMLSMMK QIEDKIEEIL SKIYHIENEI ARIKKLIGER IDGR

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: 5B3 antibody heavy chain

MacromoleculeName: 5B3 antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.245752 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLVESGGG LVKPGGSLKL SCAASGFTFS SYDMSWVRQT PEKRLEWVAM ISSGGSYSYY PDSVKGRFTI SRDNAKNTLY LQMSSLRSE DTAMYYCARQ GDYAWFAYWG QGTLVTVSSA S

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Macromolecule #3: 5B3 antibody light chain

MacromoleculeName: 5B3 antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.517844 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIQMTQSPAS QSASLGESVT ITCLASQTIG TWLAWYQQKP GKSPQLLIYA ATSLADGVPS RFSGSGSGTK FSFKISSLQA EDFVSYYCQ QFYSTPFTFG GGTKLEIK

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38721
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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