5TR8

Crystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits broad B cell responses.

Kanekiyo, M.Joyce, M.G.Gillespie, R.A.Gallagher, J.R.Andrews, S.F.Yassine, H.M.Wheatley, A.K.Fisher, B.E.Ambrozak, D.R.Creanga, A.Leung, K.Yang, E.S.Boyoglu-Barnum, S.Georgiev, I.S.Tsybovsky, Y.Prabhakaran, M.S.Andersen, H.Kong, W.P.Baxa, U.Zephir, K.L.Ledgerwood, J.E.Koup, R.A.Kwong, P.D.Harris, A.K.McDermott, A.B.Mascola, J.R.Graham, B.S.

(2019) Nat.Immunol. 20: 362-372

  • DOI: 10.1038/s41590-018-0305-x

  • PubMed Abstract: 
  • The present vaccine against influenza virus has the inevitable risk of antigenic discordance between the vaccine and the circulating strains, which diminishes vaccine efficacy. This necessitates new approaches that provide broader protection against ...

    The present vaccine against influenza virus has the inevitable risk of antigenic discordance between the vaccine and the circulating strains, which diminishes vaccine efficacy. This necessitates new approaches that provide broader protection against influenza. Here we designed a vaccine using the hypervariable receptor-binding domain (RBD) of viral hemagglutinin displayed on a nanoparticle (np) able to elicit antibody responses that neutralize H1N1 influenza viruses spanning over 90 years. Co-display of RBDs from multiple strains across time, so that the adjacent RBDs are heterotypic, provides an avidity advantage to cross-reactive B cells. Immunization with the mosaic RBD-np elicited broader antibody responses than those induced by an admixture of nanoparticles encompassing the same set of RBDs as separate homotypic arrays. Furthermore, we identified a broadly neutralizing monoclonal antibody in a mouse immunized with mosaic RBD-np. The mosaic antigen array signifies a unique approach that subverts monotypic immunodominance and allows otherwise subdominant cross-reactive B cell responses to emerge.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. kanekiyom@nih.gov.,Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Biomedical Research Center, Qatar University, Doha, Qatar.,Vanderbilt Vaccine Center and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. bgraham@nih.gov.,Cryo-EM facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Electron Microscope Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Bioqual, Inc., Rockville, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
441D6 Fab Light chain
L
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
441D6 Fab Heavy chain
H
221N/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
NI
Query on NI

Download SDF File 
Download CCD File 
L
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.463α = 90.00
b = 83.332β = 105.69
c = 83.160γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2019-08-07
    Type: Data collection, Database references