5C0S

Crystal structure of a generation 4 influenza hemagglutinin stabilized stem in complex with the broadly neutralizing antibody CR6261


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Hemagglutinin-stem nanoparticles generate heterosubtypic influenza protection.

Yassine, H.M.Boyington, J.C.McTamney, P.M.Wei, C.J.Kanekiyo, M.Kong, W.P.Gallagher, J.R.Wang, L.Zhang, Y.Joyce, M.G.Lingwood, D.Moin, S.M.Andersen, H.Okuno, Y.Rao, S.S.Harris, A.K.Kwong, P.D.Mascola, J.R.Nabel, G.J.Graham, B.S.

(2015) Nat. Med. 21: 1065-1070

  • DOI: 10.1038/nm.3927
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The antibody response to influenza is primarily focused on the head region of the hemagglutinin (HA) glycoprotein, which in turn undergoes antigenic drift, thus necessitating annual updates of influenza vaccines. In contrast, the immunogenically subd ...

    The antibody response to influenza is primarily focused on the head region of the hemagglutinin (HA) glycoprotein, which in turn undergoes antigenic drift, thus necessitating annual updates of influenza vaccines. In contrast, the immunogenically subdominant stem region of HA is highly conserved and recognized by antibodies capable of binding multiple HA subtypes. Here we report the structure-based development of an H1 HA stem-only immunogen that confers heterosubtypic protection in mice and ferrets. Six iterative cycles of structure-based design (Gen1-Gen6) yielded successive H1 HA stabilized-stem (HA-SS) immunogens that lack the immunodominant head domain. Antigenic characterization, determination of two HA-SS crystal structures in complex with stem-specific monoclonal antibodies and cryo-electron microscopy analysis of HA-SS on ferritin nanoparticles (H1-SS-np) confirmed the preservation of key structural elements. Vaccination of mice and ferrets with H1-SS-np elicited broadly cross-reactive antibodies that completely protected mice and partially protected ferrets against lethal heterosubtypic H5N1 influenza virus challenge despite the absence of detectable H5N1 neutralizing activity in vitro. Passive transfer of immunoglobulin from H1-SS-np-immunized mice to naive mice conferred protection against H5N1 challenge, indicating that vaccine-elicited HA stem-specific antibodies can protect against diverse group 1 influenza strains.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein
A
305Human immunodeficiency virus type 1 group M subtype BInfluenza A virusEnterobacteria phage T4
This entity is chimeric
Mutation(s): 0 
Gene Names: env, HA, wac
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Find proteins for Q6WG00 (Influenza A virus)
Go to UniProtKB:  Q6WG00
Find proteins for D9IEJ2 (Enterobacteria phage T4)
Go to UniProtKB:  D9IEJ2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CR6261 antibody heavy chain
H
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CR6261 antibody light chain
L
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.238 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 101.649α = 90.00
b = 101.649β = 90.00
c = 186.022γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
Cootmodel building
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references
  • Version 1.2: 2015-10-21
    Type: Source and taxonomy