4WSR

The crystal structure of hemagglutinin form A/chicken/New York/14677-13/1998

PDB DOI: https://doi.org/10.2210/pdb4WSR/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.03456-14
Primary Citation of Related Structures:
4WSR, 4WST, 4WSV

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.

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: 350.93 kDa
Atom Count: 24,430
Modelled Residue Count: 2,915
Deposited Residue Count: 3,084
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A B C D [auth E] E [auth D] 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0A3A5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

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 K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D]	K [auth A] L [auth B] M [auth C] N [auth C] O [auth C] K [auth A], L [auth B], M [auth C], N [auth C], O [auth C], P [auth E], Q [auth E], R [auth D], S [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 252.545	α = 90
b = 134.822	β = 113.23
c = 123.093	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Revision History (Full details and data files)

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