9D0Y | pdb_00009d0y

Map of endoH-treated hemagglutinin A/Sing/INFIMH/16


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift.

de Paiva Froes Rocha, R.Tomris, I.Bowman, C.A.Stevens, E.Kantorow, J.Plitt, C.M.Peng, W.Oeverdieck, S.Galdino Andrade, T.Ferguson, J.A.Jung, D.D.Marques, R.E.Herfst, S.Snijder, J.Chakraborty, S.Torrents de la Pena, A.Berndsen, Z.T.de Vries, R.P.Ward, A.B.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-66375-7
  • Primary Citation of Related Structures:  
    9CXT, 9CXU, 9D0Y, 9D1U, 9D2M

  • PubMed Abstract: 

    The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved epitopes capable of eliciting robust and durable immune responses. In this study, we explore the influence of glycan evolution on H3 hemagglutinin from 1968 to present day and its impacts on protein structure, antigenicity and immunogenicity by using computational, biochemical and biophysical techniques. Structural characterization of HK/68 and Sing/16 by cryo-electron microscopy shows that while HK/68 is resistant to enzymatic deglycosylation, removal of glycans destabilizes the hyperglycosylated head and membrane-proximal region in Sing/16. Furthermore, the appearance of glycans in Sing/16 hemagglutinin head domain shifts the polyclonal immune response upon vaccination to target the esterase and stem. These insights expand our understanding of glycans beyond their role in protein folding and highlight the interplay among glycan integration and immune recognition to design a universal influenza vaccine.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA,
C [auth B],
E [auth C]
340Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A2R4U332 (Influenza A virus)
Explore A0A2R4U332 
Go to UniProtKB:  A0A2R4U332
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R4U332
Glycosylation
Glycosylation Sites: 9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain, Green fluorescent protein fusionB [auth D],
D [auth E],
F
486Influenza A virusAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: HAGFP
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for Q38SQ8 (Influenza A virus (strain A/Hong Kong/5/1983 H3N2))
Explore Q38SQ8 
Go to UniProtKB:  Q38SQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212Q38SQ8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth F],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth D],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references