4WSS | pdb_00004wss

The crystal structure of hemagglutinin form A/chicken/New York/14677-13/1998 in complex with LSTa

• PDB DOI: https://doi.org/10.2210/pdb4WSS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/chicken/New York/14677-13/1998(H6N2))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2014-10-28 Released: 2015-02-25 
• Deposition Author(s): Yang, H., Carney, P.J., Chang, J.C., Villanueva, J.M., Stevens, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.

Yang, H., Carney, P.J., Chang, J.C., Villanueva, J.M., Stevens, J.

(2015) J Virol 89: 4612-4623

• PubMed: 25673707 
• DOI: https://doi.org/10.1128/JVI.03456-14
• Primary Citation Related Structures: 
  4WSR, 4WSS, 4WST, 4WSU, 4WSV, 4WSW, 4WSX


• PubMed Abstract: 
  

  During 2013, three new avian influenza A virus subtypes, A(H7N9), A(H6N1), and A(H10N8), resulted in human infections. While the A(H7N9) virus resulted in a significant epidemic in China across 19 provinces and municipalities, both A(H6N1) and A(H10N8) viruses resulted in only a few human infections. This study focuses on the major surface glycoprotein hemagglutinins from both of these novel human viruses. The detailed structural and glycan microarray analyses presented here highlight the idea that both A(H6N1) and A(H10N8) virus hemagglutinins retain a strong avian receptor binding preference and thus currently pose a low risk for sustained human infections. Human infections with zoonotic influenza virus subtypes continue to be a great public health concern. We report detailed structural analysis and glycan microarray data for recombinant hemagglutinins from A(H6N1) and A(H10N8) viruses, isolated from human infections in 2013, and compare them with hemagglutinins of avian origin. This is the first structural report of an H6 hemagglutinin, and our results should further the understanding of these viruses and provide useful information to aid in the continuous surveillance of these zoonotic influenza viruses.

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Organizational Affiliation: 
• Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 351.66 kDa 
• Atom Count: 23,442 
• Modeled Residue Count: 2,914 
• Deposited Residue Count: 3,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C, D [auth E], E [auth D], F	514	Influenza A virus (A/chicken/New York/14677-13/1998(H6N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q0A3A5 (Influenza A virus) Explore Q0A3A5  Go to UniProtKB:  Q0A3A5
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, K	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	L [auth B], M [auth B], N [auth C], O [auth C], P [auth E], Q [auth E], R [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: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067	H, I, K	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 254.967	α = 90
b = 134.779	β = 112.2
c = 122.622	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Yang, H., Carney, P.J., Chang, J.C., Villanueva, J.M., Stevens, J.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary