47SS | pdb_000047ss

The structure of hemagglutinin T160A mutant (H3 numbering) from H9N2 influenza virus (A/chicken/Tianjin/CAS/2007) in complex with avian receptor analog 3'SLNLN

PDB DOI: https://doi.org/10.2210/pdb47SS/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2026-10-30 Released: 2026-11-11
Deposition Author(s): Wang, M., Peng, R.C., Qi, J.X., Shi, Y., Gao, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.281 (Depositor), 0.282 (DCC)
R-Value Work:
0.253 (Depositor), 0.253 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Structural Basis of Avian-to-Human Receptor-Binding Adaptation in H9Ny Influenza A Virus Hemagglutinin

Wang, M., Zhao, C.K., Peng, R.C., Bai, S.R., Yang, W., Xu, Y., Peng, Q., Luo, H., Zhang, W., Wang, F., Liu, J.H., Qi, J.X., Shi, Y., Pu, J., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 112.55 kDa
Atom Count: 7,900
Modeled Residue Count: 956
Deposited Residue Count: 992
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin (Fragment)	A, C [auth D]	320	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7YL49 (Influenza A virus(A/swine/Henan/5/2004(H9N2))) Explore A7YL49 Go to UniProtKB: A7YL49
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7YL49
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin (Fragment)	B, D [auth E]	176	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7YL88 (Influenza A virus(A/swine/Henan/2/2004(H9N2))) Explore A7YL88 Go to UniProtKB: A7YL88
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7YL88
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	E [auth C], F	2		N/A	Interactions Focus chain E [auth C] Focus chain F Interactions & Density Focus chain E [auth C] Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.281 (Depositor), 0.282 (DCC)
R-Value Work: 0.253 (Depositor), 0.253 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.809	α = 90
b = 94.809	β = 90
c = 357.53	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32192452

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release