4WA2

The crystal structure of hemagglutinin from a H3N8 influenza virus isolated from New England harbor seals in complex with 3'SLN

PDB DOI: https://doi.org/10.2210/pdb4WA2/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/harbor seal/Massachusetts/1/2011(H3N8))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2014-08-28 Released: 2015-01-14
Deposition Author(s): Yang, H., Villanueva, J.M., Gubareva, L.V., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.236
R-Value Work: 0.184
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals.

Yang, H., Nguyen, H.T., Carney, P.J., Guo, Z., Chang, J.C., Jones, J., Davis, C.T., Villanueva, J.M., Gubareva, L.V., Stevens, J.

(2015) J Virol 89: 2801-2812

PubMed: 25540377 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.02723-14
Primary Citation of Related Structures:
4WA1, 4WA2, 4WA3, 4WA4, 4WA5

PubMed Abstract:
In late 2011, an A(H3N8) influenza virus infection resulted in the deaths of 162 New England harbor seals. Virus sequence analysis and virus receptor binding studies highlighted potential markers responsible for mammalian adaptation and a mixed receptor binding preference (S. J. Anthony, J. A. St Leger, K. Pugliares, H. S. Ip, J. M. Chan, Z. W. Carpenter, I. Navarrete-Macias, M. Sanchez-Leon, J. T. Saliki, J. Pedersen, W. Karesh, P. Daszak, R. Rabadan, T. Rowles, W. I. Lipkin, MBio 3:e00166-00112, 2012, http://dx.doi.org/10.1128/mBio.00166-12). Here, we present a detailed structural and biochemical analysis of the surface antigens of the virus. Results obtained with recombinant proteins for both the hemagglutinin and neuraminidase indicate a true avian receptor binding preference. Although the detection of this virus in new species highlights an increased potential for cross-species transmission, our results indicate that the A(H3N8) virus currently poses a low risk to humans.

Organizational Affiliation

Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

Macromolecule Content

Total Structure Weight: 343.01 kDa
Atom Count: 24,811
Modelled Residue Count: 2,946
Deposited Residue Count: 2,976
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C, D, E A, B, C, D, E, F	496	Influenza A virus (A/harbor seal/Massachusetts/1/2011(H3N8))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for I6NNE1 (Influenza A virus) Explore I6NNE1 Go to UniProtKB: I6NNE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6NNE1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K, P	3		N/A	Interactions Focus chain G Focus chain I Focus chain K Focus chain P Interactions & Density Focus chain G Focus chain I Focus chain K Focus chain P
Glycosylation Resources
GlyTouCan: G46776WR GlyCosmos: G46776WR GlyGen: G46776WR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, J, L, M, O H, J, L, M, O, Q, R, T	2		N-Glycosylation	Interactions Focus chain H Focus chain J Focus chain L Focus chain M Focus chain O Focus chain Q Focus chain R Focus chain T Interactions & Density Focus chain H Focus chain J Focus chain L Focus chain M Focus chain O Focus chain Q Focus chain R Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, S	3		N-Glycosylation	Interactions Focus chain N Focus chain S Interactions & Density Focus chain N Focus chain S
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth F] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D]	AA [auth E] BA [auth F] U [auth A] V [auth A] W [auth B] AA [auth E], BA [auth F], U [auth A], V [auth A], W [auth B], X [auth B], Y [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.236
R-Value Work: 0.184
R-Value Observed: 0.187
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.541	α = 90.02
b = 102.327	β = 90.02
c = 109.666	γ = 89.51

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-02-18
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary