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 9O8S | pdb_00009o8s

Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9O8S

This is version 1.2 of the entry. See complete history. 

Literature

B cell imprinting in children impairs antibodies to the haemagglutinin stalk.

Sun, J., Jo, G., Troxell, C.A., Fu, Y., Hoezl, R., Lv, H., Abozeid, H.H., Teo, Q.W., Pholcharee, T., McGrath, J.J.C., Changrob, S., Nelson, S.A., Yasuhara, A., Huang, M., Zheng, N.Y., Chervin, J.C., Li, L., Fernandez-Quintero, M.L., Loeffler, J.R., Rodriguez, A.J., Huang, J., Swanson, O.M., Balmaseda, A., Kuan, G., Campredon, L., Kaitlynn Allen, E., Neumann, G., Wu, N.C., Kawaoka, Y., Krammer, F., Mejias, A., Ramilo, O., Thomas, P.G., Gordon, A., Ward, A.B., Han, J., Wilson, P.C.

(2026) Nature 653: 528-537

  • DOI: https://doi.org/10.1038/s41586-026-10248-6
  • Primary Citation Related Structures: 
    9O8Q, 9O8R, 9O8S, 9O8T

  • PubMed Abstract: 

    Immune imprinting 1 or original antigenic sin 2 is a phenomenon whereby the immune system preferentially recalls its initial response to a related, often evolving pathogen after subsequent exposure. Despite its important implications for vaccine development, the causes of imprinting remain unclear. Here, to understand the basis and impact of imprinting by influenza A viruses, we characterized the B cell responses of young children after consecutive first infections with divergent H1N1 and H3N2 strains of influenza. Children had a primary but otherwise similar B cell response to that of adults. Adult B cells commonly cross-reacted with past strains using more stereotyped and mutated immunoglobulin genes, indicating substantial homosubtypic imprinting. In children, after consecutive heterosubtypic primary infections, up to 6% of memory B cells are H1/H3 cross-reactive and bind to the highly conserved central stalk epitope-a lead target for broadly protective vaccine candidates. Over 90% of these B cells had a higher affinity for the imprinting H3N2 strain, resulting in reduced breadth and neutralization potency against H1N1 strains. Mechanistically, the imprinting H3 strains and affected H1 strains shared a residue change in the stalk epitope (D46N) that was central to the nearly universal shift in reactivity, despite differing by only a single atomic group. In conclusion, imprinting by influenza viruses can cause a deleterious shift of nearly the entire memory recall response against key, conserved epitopes.


  • Organizational Affiliation: 
    • Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 283.9 kDa 
  • Atom Count: 17,628 
  • Modeled Residue Count: 2,163 
  • Deposited Residue Count: 2,454 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1A,
E [auth C],
I [auth D]
345Influenza A virus (A/Hong Kong/485197/2014(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0K0YAS1 (Influenza A virus)
Explore A0A0K0YAS1 
Go to UniProtKB:  A0A0K0YAS1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K0YAS1
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2B,
F [auth E],
J [auth F]
236Influenza A virus (A/Hong Kong/485197/2014(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0K0YAS1 (Influenza A virus)
Explore A0A0K0YAS1 
Go to UniProtKB:  A0A0K0YAS1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K0YAS1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NI04359_d30_240 Fab heavy chainC [auth H],
G,
K [auth I]
130Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NI04359_d30_240 Fab light chainD [auth L],
H [auth J],
L [auth K]
107Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, O, R, T, W
M, O, R, T, W, Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
N, S, X
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
P,
Q,
U,
V,
AA [auth a],
P,
Q,
U,
V,
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
FA [auth A]
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth B],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth E],
NA [auth D],
OA [auth D],
PA [auth D],
QA [auth D],
RA [auth D],
SA [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93019C00051

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-27
    Changes: Data collection, Database references