8TP5

H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1E04


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.

Yang, Y.R.Han, J.Perrett, H.R.Richey, S.T.Jackson, A.M.Rodriguez, A.J.Gillespie, R.A.O'Connell, S.Raab, J.E.Cominsky, L.Y.Chopde, A.Kanekiyo, M.Houser, K.V.Chen, G.L.McDermott, A.B.Andrews, S.F.Ward, A.B.

(2023) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.08.23.554525
  • Primary Citation of Related Structures:  
    8TP2, 8TP3, 8TP4, 8TP5, 8TP6, 8TP7, 8TP9, 8TPA

  • PubMed Abstract: 

    Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, G
322Influenza A virus (A/New Caledonia/20/1999(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6WG00 (Influenza A virus)
Explore Q6WG00 
Go to UniProtKB:  Q6WG00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WG00
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, I
171Influenza A virus (A/New Caledonia/20/1999(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6WG00 (Influenza A virus)
Explore Q6WG00 
Go to UniProtKB:  Q6WG00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WG00
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of Fab 1-1-1E04
E, H, J
130Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of Fab 1-1-1E04
F, K, L
112Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth G]
P [auth A]
Q [auth A]
R [auth A]
S [auth A]
AA [auth G],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth G],
Y [auth G],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2 T32 AI007244-36
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1F31Al172358

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release