Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.95 kDa 
• Atom Count: 14190 
• Modelled Residue Count: 1527 
• Deposited Residue Count: 1545 
• Unique protein chains: 1

4F23

Influenza A virus hemagglutinin H16 HA0 structure with an alpha-helix conformation in the cleavage site: a potential drug target

• PDB DOI: 10.2210/pdb4F23/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/black-headed gull/Sweden/2/99(H16N3))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-05-07 Released: 2012-11-21 
• Deposition Author(s): Lu, X., Shi, Y., Gao, F., Xiao, H., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

Insights into Avian Influenza Virus Pathogenicity: the Hemagglutinin Precursor HA0 of Subtype H16 Has an Alpha-Helix Structure in Its Cleavage Site with Inefficient HA1/HA2 Cleavage.

Lu, X., Shi, Y., Gao, F., Xiao, H., Wang, M., Qi, J., Gao, G.F.

(2012) J Virol 86: 12861-12870

• PubMed: 22993148 
• DOI: 10.1128/JVI.01606-12
• Primary Citation of Related Structures:  
  4F23, 4FIU


• PubMed Abstract: 
  

With a new serotype (H17) of hemagglutinin (HA) recently being discovered, there are now 17 serotypes (H1 to H17) of influenza A viruses in total. It is believed that HA is initially expressed as a precursor of HA0 and then cleaved into HA1 and HA2, forming a disulfide bond-linked complex, for its full function. Structural data show that a loop structure exists in the cleavage site between HA1 and HA2, and this flexible loop is crucial for the efficient cleavage of HA0. Here, the crystal structures of H16 (a low-pathogenicity avian influenza virus) in their HA0 form (H16HA0) have been solved at 1.7-Å and 2.0-Å resolutions. To our surprise, an α-helix element in the cleavage site which inserts into the negatively charged cavity with the key residue R329 hidden behind the helix was observed. In vitro trypsin cleavage experiments demonstrated inefficient cleavage of H16HA0 under both neutral and low-pH conditions. The results provide new insights into influenza A virus pathogenicity; both the relatively stable α-helix structure in the flexible cleavage loop and inaccessibility of the cleavage site likely contribute to the low pathogenicity of avian influenza A virus. Furthermore, compared to all of the HAs whose structures have been solved, H16 is a good reference for assigning the HA subtypes into two groups on the basis of the three-dimensional structure, which is consistent with the phylogenetic grouping. We conclude that in light of the current H16HA0 structure, the natural α-helix element might provide a new opportunity for influenza virus inhibitor design.

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Organizational Affiliation: 

College of Veterinary Medicine, China Agricultural University, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	515	Influenza A virus (A/black-headed gull/Sweden/2/99(H16N3))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q5DL24 (Influenza A virus) Explore Q5DL24  Go to UniProtKB:  Q5DL24

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.332	α = 90
b = 240.944	β = 119.79
c = 69.673	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-07 
• Released Date: 2012-11-21 
Deposition Author(s): Lu, X., Shi, Y., Gao, F., Xiao, H., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary