4F3Z

Crystal structure of a swine H1N2 influenza virus hemagglutinin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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Literature

Functional Balance of the Hemagglutinin and Neuraminidase Activities Accompanies the Emergence of the 2009 H1N1 Influenza Pandemic.

Xu, R., Zhu, X., McBride, R., Nycholat, C.M., Yu, W., Paulson, J.C., Wilson, I.A.

(2012) J Virol 86: 9221-9232

  • DOI: 10.1128/JVI.00697-12
  • Primary Citation of Related Structures:  
    4F3Z

  • PubMed Abstract: 

    • The 2009 H1N1 influenza pandemic is the first human pandemic in decades and was of swine origin. Although swine are believed to be an intermediate host in the emergence of new human influenza viruses, there is still little known about the host barriers that keep swine influenza viruses from entering the human population ...

    The 2009 H1N1 influenza pandemic is the first human pandemic in decades and was of swine origin. Although swine are believed to be an intermediate host in the emergence of new human influenza viruses, there is still little known about the host barriers that keep swine influenza viruses from entering the human population. We surveyed swine progenitors and human viruses from the 2009 pandemic and measured the activities of the hemagglutinin (HA) and neuraminidase (NA), which are the two viral surface proteins that interact with host glycan receptors. A functional balance of these two activities (HA binding and NA cleavage) is found in human viruses but not in the swine progenitors. The human 2009 H1N1 pandemic virus exhibited both low HA avidity for glycan receptors as a result of mutations near the receptor binding site and weak NA enzymatic activity. Thus, a functional match between the hemagglutinin and neuraminidase appears to be necessary for efficient transmission between humans and may be an indicator of the pandemic potential of zoonotic viruses.

    Organizational Affiliation: 

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA, C, E329Influenza A virus (A/Swine/Indiana/P12439/00 (H1N2))Mutation(s): 2 
Gene Names: HA
UniProt
Find proteins for Q8QT89 (Influenza A virus)
Explore Q8QT89 
Go to UniProtKB:  Q8QT89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8QT89
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB, D, F179Influenza A virus (A/Swine/Indiana/P12439/00 (H1N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q8QT89 (Influenza A virus)
Explore Q8QT89 
Go to UniProtKB:  Q8QT89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8QT89
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
G [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.44α = 90
b = 94.92β = 90
c = 220.53γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-05-09 
  • Released Date: 2012-07-04 
    • Deposition Author(s): Xu, R., Wilson, I.A.

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary