6U1T

Crystal structure of anti-Nipah virus (NiV) F 5B3 antibody Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.483 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections.

Dang, H.V.Chan, Y.P.Park, Y.J.Snijder, J.Da Silva, S.C.Vu, B.Yan, L.Feng, Y.R.Rockx, B.Geisbert, T.W.Mire, C.E.Broder, C.C.Veesler, D.

(2019) Nat.Struct.Mol.Biol. 26: 980-987

  • DOI: 10.1038/s41594-019-0308-9
  • Primary Citation of Related Structures:  

  • PubMed 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 therapeutics currently exist to protect humans agains ...

    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.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA.,Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands.,Sealy Center for Vaccine Development, Departments of Pathology and Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, USA.,Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA. christopher.broder@usuhs.edu.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dveesler@uw.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
antigen-binding (Fab) fragment, heavy chain
H
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antigen-binding (Fab) fragment, light chain
L
214N/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
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.483 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.137 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.120α = 90.00
b = 95.010β = 90.00
c = 137.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM120553

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Database references
  • Version 1.2: 2019-11-27
    Type: Database references