Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 179.68 kDa 
• Atom Count: 12,735 
• Modelled Residue Count: 1,473 
• Deposited Residue Count: 1,509 
• Unique protein chains: 2

 2YPG

Haemagglutinin of 1968 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc

• PDB DOI: 10.2210/pdb2YPG/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/X-31(H3N2))
• Mutation(s): No 


• Deposited: 2012-10-30 Released: 2012-11-07 
• Deposition Author(s): Liu, J., Xiong, X., Haire, L.F., Lin, Y.P., Wharton, S.A., Martin, S.R., Coombs, P.J., Vachieri, S.G., Christodoulou, E., Walker, P.A., Skehel, J.J., Gamblin, S.J., Hay, A.J., Daniels, R.S., McCauley, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.190 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Evolution of the Receptor Binding Properties of the Influenza A(H3N2) Hemagglutinin.

Lin, Y.P., Xiong, X., Wharton, S.A., Martin, S.R., Coombs, P.J., Vachieri, S.G., Christodoulou, E., Walker, P.A., Liu, J., Skehel, J.J., Gamblin, S.J., Hay, A.J., Daniels, R.S., Mccauley, J.W.

(2012) Proc Natl Acad Sci U S A 109: 21474

• PubMed: 23236176 
• DOI: 10.1073/pnas.1218841110
• Primary Citation of Related Structures:  
  2YP2, 2YP3, 2YP4, 2YP5, 2YP7, 2YP8, 2YP9, 2YPG


• PubMed Abstract: 
  

The hemagglutinin (HA) of influenza A(H3N2) virus responsible for the 1968 influenza pandemic derived from an avian virus. On introduction into humans, its receptor binding properties had changed from a preference for avian receptors (α2,3-linked sialic acid) to a preference for human receptors (α2,6-linked sialic acid). By 2001, the avidity of human H3 viruses for avian receptors had declined, and since then the affinity for human receptors has also decreased significantly. These changes in receptor binding, which correlate with increased difficulties in virus propagation in vitro and in antigenic analysis, have been assessed by virus hemagglutination of erythrocytes from different species and quantified by measuring virus binding to receptor analogs using surface biolayer interferometry. Crystal structures of HA-receptor analog complexes formed with HAs from viruses isolated in 2004 and 2005 reveal significant differences in the conformation of the 220-loop of HA1, relative to the 1968 structure, resulting in altered interactions between the HA and the receptor analog that explain the changes in receptor affinity. Site-specific mutagenesis shows the HA1 Asp-225→Asn substitution to be the key determinant of the decreased receptor binding in viruses circulating since 2005. Our results indicate that the evolution of human influenza A(H3N2) viruses since 1968 has produced a virus with a low propensity to bind human receptor analogs, and this loss of avidity correlates with the marked reduction in A(H3N2) virus disease impact in the last 10 y.

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Organizational Affiliation: 

Division of Virology, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ HA1 CHAIN	A, C, E	328	Influenza A virus (A/X-31(H3N2))	Mutation(s): 0
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437  Go to UniProtKB:  P03437

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ HA2 CHAIN	B, D, F	175	Influenza A virus (A/X-31(H3N2))	Mutation(s): 0
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437  Go to UniProtKB:  P03437

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28454KX GlyCosmos:  G28454KX GlyGen:  G28454KX

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, M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, K, L, N, Q	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	J, R	5		N/A
Glycosylation Resources
GlyTouCan:  G83513YI GlyCosmos:  G83513YI GlyGen:  G83513YI

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	O	4		N/A
Glycosylation Resources
GlyTouCan:  G03509EL GlyCosmos:  G03509EL GlyGen:  G03509EL

Entity ID: 8
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G53081KU GlyCosmos:  G53081KU GlyGen:  G53081KU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	CA [auth D], EA [auth E], IA [auth F], S [auth A], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC	AA [auth C], BA [auth C], DA [auth D], FA [auth E], GA [auth E], HA [auth E], JA [auth F], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B], Z [auth C]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.190 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.767	α = 90
b = 160.767	β = 90
c = 177.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Liu, J., Xiong, X., Haire, L.F., Lin, Y.P., Wharton, S.A., Martin, S.R., Coombs, P.J., Vachieri, S.G., Christodoulou, E., Walker, P.A., Skehel, J.J., Gamblin, S.J., Hay, A.J., Daniels, R.S., McCauley, J.W.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-12-26
  Changes: Database references, Structure summary
• Version 1.2: 2013-01-16
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary