6T3F

Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex.

Avanzato, V.A.Oguntuyo, K.Y.Escalera-Zamudio, M.Gutierrez, B.Golden, M.Kosakovsky Pond, S.L.Pryce, R.Walter, T.S.Seow, J.Doores, K.J.Pybus, O.G.Munster, V.J.Lee, B.Bowden, T.A.

(2019) Proc.Natl.Acad.Sci.USA --: --

  • DOI: 10.1073/pnas.1912503116

  • PubMed Abstract: 
  • Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes frequent outbreaks of severe neurologic and respiratory disease in humans with high case fatality rates. The 2 glycoproteins displayed on the surface of the virus, NiV-G and NiV-F, me ...

    Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes frequent outbreaks of severe neurologic and respiratory disease in humans with high case fatality rates. The 2 glycoproteins displayed on the surface of the virus, NiV-G and NiV-F, mediate host-cell attachment and membrane fusion, respectively, and are targets of the host antibody response. Here, we provide a molecular basis for neutralization of NiV through antibody-mediated targeting of NiV-F. Structural characterization of a neutralizing antibody (nAb) in complex with trimeric prefusion NiV-F reveals an epitope at the membrane-distal domain III (DIII) of the molecule, a region that undergoes substantial refolding during host-cell entry. The epitope of this monoclonal antibody (mAb66) is primarily protein-specific and we observe that glycosylation at the periphery of the interface likely does not inhibit mAb66 binding to NiV-F. Further characterization reveals that a Hendra virus-F-specific nAb (mAb36) and many antibodies in an antihenipavirus-F polyclonal antibody mixture (pAb835) also target this region of the molecule. Integrated with previously reported paramyxovirus F-nAb structures, these data support a model whereby the membrane-distal region of the F protein is targeted by the antibody-mediated immune response across henipaviruses. Notably, our domain-specific sequence analysis reveals no evidence of selective pressure at this region of the molecule, suggestive that functional constraints prevent immune-driven sequence variation. Combined, our data reveal the membrane-distal region of NiV-F as a site of vulnerability on the NiV surface.


    Organizational Affiliation

    Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; Benhur.Lee@mssm.edu thomas.bowden@strubi.ox.ac.uk.,Department of Zoology, Oxford University, OX1 3PS Oxford, United Kingdom.,Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom; Benhur.Lee@mssm.edu thomas.bowden@strubi.ox.ac.uk.,Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122.,Department of Infectious Diseases, King's College London, Guy's Hospital, SE1 9RT London, United Kingdom.,Global Virus Network (GVN) Center of Excellence, Center for Virology, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion glycoprotein F0
F
502Nipah virusMutation(s): 0 
Gene Names: F
Find proteins for Q9IH63 (Nipah virus)
Go to UniProtKB:  Q9IH63
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab66 light chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab66 heavy chain
H
228N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
F, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 149.249α = 90.00
b = 149.249β = 90.00
c = 385.392γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/S007555/1
Medical Research Council (United Kingdom)United KingdomMR/L009528/1
Medical Research Council (United Kingdom)United KingdomMR/N002091/1

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references