Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

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

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.60 kDa 
• Atom Count: 4145 
• Modelled Residue Count: 481 
• Deposited Residue Count: 501 
• Unique protein chains: 2

1JSO

STRUCTURE OF AVIAN H5 HAEMAGGLUTININ BOUND TO LSTC RECEPTOR ANALOG

• PDB DOI: 10.2210/pdb1JSO/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Mutation(s): No 


• Deposited: 2001-08-17 Released: 2001-09-26 
• Deposition Author(s): Ha, Y., Stevens, D.J., Skehel, J.J., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs.

Ha, Y., Stevens, D.J., Skehel, J.J., Wiley, D.C.

(2001) Proc Natl Acad Sci U S A 98: 11181-11186

• PubMed: 11562490 
• DOI: 10.1073/pnas.201401198
• Primary Citation of Related Structures:  
  1JSH, 1JSI, 1JSN, 1JSO


• PubMed Abstract: 
  

The three-dimensional structures of avian H5 and swine H9 influenza hemagglutinins (HAs) from viruses closely related to those that caused outbreaks of human disease in Hong Kong in 1997 and 1999 were determined bound to avian and human cell receptor analogs. Emerging influenza pandemics have been accompanied by the evolution of receptor-binding specificity from the preference of avian viruses for sialic acid receptors in alpha2,3 linkage to the preference of human viruses for alpha2,6 linkages. The four new structures show that HA binding sites specific for human receptors appear to be wider than those preferring avian receptors and how avian and human receptors are distinguished by atomic contacts at the glycosidic linkage. alpha2,3-Linked sialosides bind the avian HA in a trans conformation to form an alpha2,3 linkage-specific motif, made by the glycosidic oxygen and 4-OH of the penultimate galactose, that is complementary to the hydrogen-bonding capacity of Gln-226, an avian-specific residue. alpha2,6-Linked sialosides bind in a cis conformation, exposing the glycosidic oxygen to solution and nonpolar atoms of the receptor to Leu-226, a human-specific residue. The new structures are compared with previously reported crystal structures of HA/sialoside complexes of the H3 subtype that caused the 1968 Hong Kong Influenza virus pandemic and analyzed in relation to HA sequences of all 15 subtypes and to receptor affinity data to make clearer how receptor-binding sites of HAs from avian viruses evolve as the virus adapts to humans.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ (HA1 CHAIN)	A	325	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for A5Z226 (Influenza A virus (strain A/Duck/Singapore/3/1997 H5N3)) Explore A5Z226  Go to UniProtKB:  A5Z226

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ (HA2 CHAIN)	B	176	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for A5Z226 (Influenza A virus (strain A/Duck/Singapore/3/1997 H5N3)) Explore A5Z226  Go to UniProtKB:  A5Z226

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	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	H [auth A]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.902	α = 90
b = 130.902	β = 90
c = 254.409	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-17 
• Released Date: 2001-09-26 
Deposition Author(s): Ha, Y., Stevens, D.J., Skehel, J.J., Wiley, D.C.

Revision History  

• Version 1.0: 2001-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary