Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 176.77 kDa 
• Atom Count: 12093 
• Residue Count: 1480 
• Unique protein chains: 2

3S11

Crystal structure of H5N1 influenza virus hemagglutinin, strain 437-10

• DOI: 10.2210/pdb3S11/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-05-14 Released: 2011-12-14 
• Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Heath, R.J., White, S.W., Russell, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Acid stability of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity.

DuBois, R.M., Zaraket, H., Reddivari, M., Heath, R.J., White, S.W., Russell, C.J.

(2011) PLoS Pathog 7: e1002398-e1002398

• PubMed: 22144894 
• DOI: 10.1371/journal.ppat.1002398
• Primary Citation of Related Structures:  
  3S11, 3S12, 3S13


• PubMed Abstract: 
  

Highly pathogenic avian influenza viruses of the H5N1 subtype continue to threaten agriculture and human health. Here, we use biochemistry and x-ray crystallography to reveal how amino-acid variations in the hemagglutinin (HA) protein contribute to the pathogenicity of H5N1 influenza virus in chickens. HA proteins from highly pathogenic (HP) A/chicken/Hong Kong/YU562/2001 and moderately pathogenic (MP) A/goose/Hong Kong/437-10/1999 isolates of H5N1 were found to be expressed and cleaved in similar amounts, and both proteins had similar receptor-binding properties. However, amino-acid variations at positions 104 and 115 in the vestigial esterase sub-domain of the HA1 receptor-binding domain (RBD) were found to modulate the pH of HA activation such that the HP and MP HA proteins are activated for membrane fusion at pH 5.7 and 5.3, respectively. In general, an increase in H5N1 pathogenicity in chickens was found to correlate with an increase in the pH of HA activation for mutant and chimeric HA proteins in the observed range of pH 5.2 to 6.0. We determined a crystal structure of the MP HA protein at 2.50 Å resolution and two structures of HP HA at 2.95 and 3.10 Å resolution. Residues 104 and 115 that modulate the acid stability of the HA protein are situated at the N- and C-termini of the 110-helix in the vestigial esterase sub-domain, which interacts with the B loop of the HA2 stalk domain. Interactions between the 110-helix and the stalk domain appear to be important in regulating HA protein acid stability, which in turn modulates influenza virus replication and pathogenesis. Overall, an optimal activation pH of the HA protein is found to be necessary for high pathogenicity by H5N1 influenza virus in avian species.

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Organizational Affiliation: 

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	331	Influenza A virus	Mutation(s): 0
Find proteins for Q9Q0U6 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0U6  Go to UniProtKB:  Q9Q0U6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	182	Influenza A virus	Mutation(s): 0
Find proteins for Q8QPL1 (Influenza A virus (strain A/Duck/Hong Kong/2986.1/2000 H5N1 genotype C)) Explore Q8QPL1  Go to UniProtKB:  Q8QPL1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I	2		N/A

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, C, E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TAM	A	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N
GOL	A, C, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.365	α = 90
b = 241.054	β = 116.69
c = 70.061	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-14 
• Released Date: 2011-12-14 
Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Heath, R.J., White, S.W., Russell, C.J.

Revision History 

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary