8VEE | pdb_00008vee

Cryo-EM structure of antibody T5-1E08 in complex with H7N9 Influenza Hemagglutinin Trimer (A/Shanghai/2/13)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages.

Mantus, G.E.Cerutti, G.Chambers, M.Gillespie, R.A.Shimberg, G.D.Spangler, A.Gorman, J.Zhou, T.Shen, C.H.Kanekiyo, M.Kwong, P.D.Shapiro, L.Andrews, S.F.

(2025) Structure 33: 869

  • DOI: https://doi.org/10.1016/j.str.2025.02.010
  • Primary Citation of Related Structures:  
    8T1G, 8VEB, 8VED, 8VEE, 8VEF

  • PubMed Abstract: 

    Elicitation of antibodies to the influenza hemagglutinin stem is a critical part of universal influenza vaccine strategies. While numerous broadly reactive stem antibodies have been isolated, our understanding of how these antibodies mature within the human B cell repertoire is limited. Here, we isolated and tracked two stem-specific antibody lineages over a decade in a single participant that received multiple seasonal and pandemic influenza vaccinations. Despite similar binding and neutralization profiles, antibodies from these lineages utilized fundamentally different interactions to engage the central epitope on the influenza stem. Structural analysis of an unmutated common ancestor from one lineage identified critical residues that were the main drivers of increased affinity and breadth to group 1 influenza subtypes. These observations demonstrate the heterogeneous pathways by which stem-specific antibodies can mature within the human B cell repertoire.


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

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininA,
D [auth C],
G [auth E]
560Influenza A virusMutation(s): 0 
UniProt
Find proteins for A4U7A6 (Influenza A virus (strain A/USA:Albany/12/1951 H1N1))
Explore A4U7A6 
Go to UniProtKB:  A4U7A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4U7A6
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T5-1E08 Fab heavy chainB [auth H],
E [auth G],
H [auth J]
238Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T5-1E08 Fab light chainC [auth L],
F [auth I],
I [auth K]
214Homo 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: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth M],
K [auth N],
L [auth O],
M [auth P],
N [auth Q],
J [auth M],
K [auth N],
L [auth O],
M [auth P],
N [auth Q],
O [auth R],
P [auth S],
Q [auth T],
R [auth U]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references
  • Version 1.3: 2025-05-14
    Changes: Data collection, Database references