9NRT | pdb_00009nrt

Crystal structure of the H5 influenza virus hemagglutinin from A/duck/France/161108h/2016 (H5N8) clade 2.3.4.4b in complex with O-linked glycan 25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.189 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The receptor binding properties of H5Ny influenza A viruses have evolved to bind to avian-type mucin-like O-glycans.

Weber, J.Ponse, N.L.D.Zhu, X.Carrasco, M.R.Han, A.X.Funk, M.Lin, T.H.Garcia, A.G.Spruit, C.M.Zhang, D.Yu, W.Wilson, I.A.Richard, M.Boons, G.J.de Vries, R.P.

(2026) PLoS Pathog 22: e1013812-e1013812

  • DOI: https://doi.org/10.1371/journal.ppat.1013812
  • Primary Citation of Related Structures:  
    9NRR, 9NRS, 9NRT, 9NRU, 9NRV

  • PubMed Abstract: 

    Highly pathogenic H5Ny influenza A viruses are causing unprecedented, season-independent outbreaks across avian and mammalian species, including dairy cattle, a novel reservoir. The sialoside-binding properties of influenza A hemagglutinin (HA) are strongly related to its ability to infect and transmit between hosts. Mucin-like O-glycans, omnipresent in respiratory tracts, have been understudied as viral receptors due to their complexity. To address this, we synthesized 25 O-linked glycans with diverse sialosides, including modifications by fucosides and sulfates. Our findings reveal that H5Ny 2.3.4.4b viruses bind core 3 sialyl-Lewisx and Sia-Gal-β3GalNAc, O-linked glycans not recognized by classical H5 or other avian viruses. By determining crystal structures, we resolved the structural features of four glycans in an H5 hemagglutinin (HA) from a 2016 2.3.4.4b virus. While these viruses do not bind human-type receptors, their broad receptor specificity enhances binding to human tracheal tissues, suggesting that O-glycan recognition could contribute to the continues spillover of this clade.


  • Organizational Affiliation
    • Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg Utrecht, Utrecht, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
329Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A6M2RJB8 (Influenza A virus)
Explore A0A6M2RJB8 
Go to UniProtKB:  A0A6M2RJB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M2RJB8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
181Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A6M2RJB8 (Influenza A virus)
Explore A0A6M2RJB8 
Go to UniProtKB:  A0A6M2RJB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M2RJB8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide linker
G, H, I, J
5Homo sapiensMutation(s): 0 
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
L
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
M, O
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
P
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
Q
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranoseR [auth l]4N/A
Glycosylation Resources
GlyTouCan:  G64844ET
GlyCosmos:  G64844ET
GlyGen:  G64844ET
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranoseS [auth R],
T [auth S],
U [auth T],
V [auth U]
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G00035MO
GlyCosmos:  G00035MO
GlyGen:  G00035MO
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
FB [auth E],
OA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CA [auth A]
CB [auth C]
DA [auth A]
AB [auth C],
BB [auth C],
CA [auth A],
CB [auth C],
DA [auth A],
DB [auth C],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
PB [auth E],
QB [auth E],
RB [auth E],
SB [auth E],
TB [auth E],
UB [auth E],
VA [auth C],
VB [auth E],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
EB [auth D]
GB [auth E]
HB [auth E]
AA [auth A],
BA [auth A],
EB [auth D],
GB [auth E],
HB [auth E],
IB [auth E],
JB [auth E],
KB [auth E],
LB [auth E],
MA [auth B],
MB [auth E],
NA [auth B],
NB [auth E],
OB [auth E],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
W [auth A],
WB [auth F],
X [auth A],
XB [auth F],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.189 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.17α = 90
b = 171.615β = 90
c = 226.424γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93021C00015 / PENN CEIRR

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references