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 9BU8 | pdb_00009bu8

Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BU8

This is version 1.1 of the entry. See complete history. 

Literature

Vaccination with different group 2 influenza subtypes alters epitope targeting and breadth of hemagglutinin stem-specific human B cells.

Mantus, G.E., Chopde, A.J., Gorman, J., Cominsky, L.Y., Ourahmane, A., Creanga, A., Shimberg, G.D., Gillespie, R.A., Van Wazer, D.J., Zhou, T., Gajjala, S.R., Williams, C., Maestle, E., Reed, D.S., Serebryannyy, L., Costner, P., Holman, L., Casazza, J.P., Koup, R.A., Dropulic, L.K., Kwong, P.D., McDermott, A.B., Kanekiyo, M., Andrews, S.F.

(2025) Sci Transl Med 17: eadr8373-eadr8373

  • DOI: https://doi.org/10.1126/scitranslmed.adr8373
  • Primary Citation Related Structures: 
    9BU6, 9BU8

  • PubMed Abstract: 

    The conserved influenza hemagglutinin stem, which is a target of cross-neutralizing antibodies, is now used in vaccine strategies focused on protecting against influenza pandemics. Antibody responses to group 1 stem have been extensively characterized, but little is known about group 2. Here, we characterized the stem-specific repertoire of individuals vaccinated with one of three group 2 influenza subtypes (H3, H7, or H10). Epitope mapping revealed two epitope supersites on the group 2 stem. Antibodies targeting the central epitope were broadly cross-reactive, whereas antibodies targeting the lower epitope had narrower breadth but higher potency against H3 subtypes. The ratio of B cells targeting each of the supersites varied with the vaccine subtype, leading to differences in the cross-reactivity of the B cell response. Our findings suggest that vaccine strategies targeting both group 2 stem epitopes would be complementary, eliciting broader and more potent protection against both seasonal and pandemic influenza strains.


  • Organizational Affiliation: 
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA.

Macromolecule Content 

  • Total Structure Weight: 263.98 kDa 
  • Atom Count: 17,109 
  • Modeled Residue Count: 2,175 
  • Deposited Residue Count: 2,349 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1
A, E, J
325Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A059T4A1 (Influenza A virus)
Explore A0A059T4A1 
Go to UniProtKB:  A0A059T4A1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059T4A1
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2
B, G, L
230Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0B4UV34 (Influenza A virus)
Explore A0A0B4UV34 
Go to UniProtKB:  A0A0B4UV34
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4UV34
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab c115.131 heavy chain
C, F, I
121Homo 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
Fab c115.131 light chain
D, H, 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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N, O
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
P [auth A]
Q [auth B]
R [auth B]
S [auth E]
T [auth G]
P [auth A],
Q [auth B],
R [auth B],
S [auth E],
T [auth G],
U [auth G],
V [auth J],
W [auth L],
X [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev_5278

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Simons FoundationUnited StatesSF349247

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references