9CXT | pdb_00009cxt

Hemagglutinin A/Hong Kong/1/68 produced in GnTI- cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CXT

This is version 1.2 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 16: 11452-11452

  • DOI: https://doi.org/10.1038/s41467-025-66375-7
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 287.77 kDa 
  • Atom Count: 11,613 
  • Modeled Residue Count: 1,446 
  • Deposited Residue Count: 2,538 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA,
E [auth C],
F [auth E]
352Influenza A virus (A/Hong Kong/1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91MA7
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain,Green fluorescent protein fusionB,
C [auth D],
D [auth F]
494Influenza A virus (A/Hong Kong/1/1968(H3N2))Aequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: HAGFP
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91MA7
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth D],
N [auth F],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth E],
U [auth E],
V [auth E],
W [auth E],
X [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: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

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: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-07
    Changes: Data collection, Database references