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 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41590-018-0305-x
  • Primary Citation of Related Structures:  
    5TR8

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
441D6 Fab Light chainA [auth L]212Mus musculusMutation(s): 0 
UniProt
Find proteins for Q7TS98 (Mus musculus)
Explore Q7TS98 
Go to UniProtKB:  Q7TS98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7TS98
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
441D6 Fab Heavy chainB [auth H]221Mus musculusMutation(s): 0 
UniProt
Find proteins for A0A0E4B366 (Mus musculus)
Explore A0A0E4B366 
Go to UniProtKB:  A0A0E4B366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E4B366
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.463α = 90
b = 83.332β = 105.69
c = 83.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description