9CJZ | pdb_00009cjz

CryoEM structure of NC99 hemagglutinin trimer in complex with Fab T009 3-E04


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Functional, Immunogenetic, and Structural Convergence in Influenza Immunity between Humans and Macaques.

Sangesland, M.Li, N.Tsybovsky, Y.Rodgers, M.D.Han, J.Rodriguez, A.J.Ferguson, J.A.Henry, A.R.Smith, S.C.Roberts-Torres, J.Gillespie, R.A.Liu, C.Merriam, J.S.Stephens, T.Williams, C.Maestle, E.Corcoran, M.Ravichandran, M.Creanga, A.Andrews, S.F.Pierson, T.C.Karlsson Hedestam, G.B.Schramm, C.A.Reed, D.S.Douek, D.C.Zhou, T.Ward, A.B.Kanekiyo, M.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.02.21.639368
  • Primary Citation of Related Structures:  
    9CJY, 9CJZ

  • PubMed Abstract: 

    Human B cell immunity to the influenza hemagglutinin (HA) stem region, a universal influenza vaccine target, is often stereotyped and immunogenetically restricted, posing challenges for study outside humans. Here, we show that macaques vaccinated with a HA stem immunogen elicit human-like public B cell lineages targeting two major conserved sites of vulnerability, the central stem and anchor epitopes. Central stem antibodies were predominantly derived from V H 1-138, the macaque homolog of human V H 1-69, a V H -gene preferentially used in human central stem broadly neutralizing antibodies (bnAbs). Similarly, macaques produced anchor bnAbs with the human-like NWP motif. Both bnAb lineages were functionally and structurally analogous to their human counterparts, with recognition mediated largely by germline-encoded motifs. Thus the macaque immunoglobulin repertoire supports human-like public bnAb responses to influenza HA. Moreover, this underscores the utility of homologous germline-encoded immunity, suggesting that immune repertoires of macaques and humans may have been similarly shaped during evolution. Functional human-like public antibody lineages can be elicited to HA stem supersites in macaques. Macaque central stem bnAbs are predominantly derived from V H 1-138, a V H -gene homologous to human V H 1-69. The human-like CDR L3 NWP anchor epitope-targeting lineage can be elicited in macaques.Central stem and anchor bnAbs from humans and macaques engage their respective epitopes with atomic level similarity.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
326Influenza A virusMutation(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, F
222Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6WG00 (Influenza A virus)
Explore Q6WG00 
Go to UniProtKB:  Q6WG00
Entity Groups  
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UniProt GroupQ6WG00
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
3-E04 Heavy chainG [auth H],
H [auth J],
K [auth M]
122Macaca fascicularisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
3-E04 Light chainI [auth K],
J [auth L],
L [auth N]
108Macaca fascicularisMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20
RECONSTRUCTIONcryoSPARC4.3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release