Biological Assembly 1  

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

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 119.28 kDa 
• Atom Count: 8005 
• Modelled Residue Count: 986 
• Deposited Residue Count: 1050 
• Unique protein chains: 2

5TG9

Crystal structure of H15 hemagglutinin from A/shearwater/WA/2576/1979 H15N9 influenza virus in complex with 3'-SLN

• PDB DOI: 10.2210/pdb5TG9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/shearWater/Australia/2576/1979(H15N9))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-09-27 Released: 2017-04-12 
• Deposition Author(s): Wilson, I.A., Tzarum, N.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.275 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Unique Structural Features of Influenza Virus H15 Hemagglutinin.

Tzarum, N., McBride, R., Nycholat, C.M., Peng, W., Paulson, J.C., Wilson, I.A.

(2017) J Virol 91

• PubMed: 28404848 
• DOI: 10.1128/JVI.00046-17
• Primary Citation of Related Structures:  
  5TG8, 5TG9


• PubMed Abstract: 
  

Influenza A H15 viruses are members of a subgroup (H7-H10-H15) of group 2 hemagglutinin (HA) subtypes that include H7N9 and H10N8 viruses that were isolated from humans during 2013. The isolation of avian H15 viruses is, however, quite rare and, until recently, geographically restricted to wild shorebirds and waterfowl in Australia. The HAs of H15 viruses contain an insertion in the 150-loop (loop beginning at position 150) of the receptor-binding site common to this subgroup and a unique insertion in the 260-loop compared to any other subtype. Here, we show that the H15 HA has a high preference for avian receptor analogs by glycan array analyses. The H15 HA crystal structure reveals that it is structurally closest to H7N9 HA, but the head domain of the H15 trimer is wider than all other HAs due to a tilt and opening of the HA1 subunits of the head domain. The extended 150-loop of the H15 HA retains the conserved conformation as in H7 and H10 HAs. Furthermore, the elongated 260-loop increases the exposed HA surface and can contribute to antigenic variation in H15 HAs. Since avian-origin H15 HA viruses have been shown to cause enhanced disease in mammalian models, further characterization and immune surveillance of H15 viruses are warranted. IMPORTANCE In the last 2 decades, an apparent increase has been reported for cases of human infection by emerging avian influenza A virus subtypes, including H7N9 and H10N8 viruses isolated during 2013. H15 is the other member of the subgroup of influenza A virus group 2 hemagglutinins (HAs) that also include H7 and H10. H15 viruses have been restricted to Australia, but recent isolation of H15 viruses in western Siberia suggests that they could be spread more globally via the avian flyways that converge and emanate from this region. Here we report on characterization of the three-dimensional structure and receptor specificity of the H15 hemagglutinin, revealing distinct features and specificities that can aid in global surveillance of such viruses for potential spread and emerging threat to the human population.

---

Organizational Affiliation: 

Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C	332	Influenza A virus (A/shearWater/Australia/2576/1979(H15N9))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for L0L3X3 (Influenza A virus) Explore L0L3X3  Go to UniProtKB:  L0L3X3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D	193	Influenza A virus (A/shearWater/Australia/2576/1979(H15N9))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for L0L3X3 (Influenza A virus) Explore L0L3X3  Go to UniProtKB:  L0L3X3

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	E, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	F	2		N/A
Glycosylation Resources
GlyTouCan:  G30207PZ GlyCosmos:  G30207PZ GlyGen:  G30207PZ

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N/A
Glycosylation Resources
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067	H	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.275 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.677	α = 90
b = 116.677	β = 90
c = 129.108	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-27 
• Released Date: 2017-04-12 
Deposition Author(s): Wilson, I.A., Tzarum, N.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI114730

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references
• Version 1.2: 2017-06-07
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary