Crystal structure of a computationally optimized H5 influenza hemagglutinin

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

Starting Model: experimental
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Structural and antigenic characterization of a computationally-optimized H5 hemagglutinin influenza vaccine.

Bar-Peled, Y.Huang, J.Nunez, I.A.Pierce, S.R.Ecker, J.W.Ross, T.M.Mousa, J.J.

(2019) Vaccine 37: 6022-6029

  • DOI: https://doi.org/10.1016/j.vaccine.2019.08.062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Influenza A virus is a leading cause of death worldwide. Viruses of the H5 subtype have the potential to induce high mortality, and no vaccines are currently available to protect against H5 influenza viruses in the event of an outbreak. Experimental vaccination with one clade 2 virus does not protect against other subclades. The computationally optimized broadly reactive (COBRA) methodology was previously used to generate a H5 hemagglutinin (HA) antigen (COBRA2) that elicited increased serological breadth against multiple clade 2 H5N1 influenza viruses. In this report, we structurally and antigenically characterized the COBRA2 HA antigen. We examined the biochemical characteristics of the COBRA2 protein and determined the protein is correctly cleaved, properly folded into a trimeric structure, and antigenically correct by probing with HA head- and stem-specific monoclonal antibodies (mAbs). We further probed the antigenicity by examining binding of a panel of H5 mouse mAbs to the COBRA2 antigen, as well as several other HA antigens. We determined the X-ray crystal structure of the COBRA2 HA antigen to 2.8 Å and the protein was observed to be in the expected trimeric form. The COBRA2 HA was structurally similar to the naturally occurring H5 HA antigens and suggests the protein folds similar to known HA structures. Overall, our data allow us to formulate a hypothesis on the mechanism of increased breadth due to vaccination with the COBRA2 HA antigen, which is that the protein incorporates antigenic sites from numerous HA antigens, and elicits mAbs with limited breadth, but with diversity in targeted antigenic sites.

  • Organizational Affiliation

    Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin557unidentified influenza virusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation Sites: 5
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
B, C
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
C8 H15 N O6
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
C4 H10 O3
Query on MG

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
N [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.518α = 90
b = 101.518β = 90
c = 450.084γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary