6XSK

Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with Stabilized SI06 (A/Solomon Islands/3/06) Influenza Hemagglutinin Trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 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

Co-immunization with hemagglutinin stem immunogens elicits cross-group neutralizing antibodies and broad protection against influenza A viruses.

Moin, S.M.Boyington, J.C.Boyoglu-Barnum, S.Gillespie, R.A.Cerutti, G.Cheung, C.S.Cagigi, A.Gallagher, J.R.Brand, J.Prabhakaran, M.Tsybovsky, Y.Stephens, T.Fisher, B.E.Creanga, A.Ataca, S.Rawi, R.Corbett, K.S.Crank, M.C.Karlsson Hedestam, G.B.Gorman, J.McDermott, A.B.Harris, A.K.Zhou, T.Kwong, P.D.Shapiro, L.Mascola, J.R.Graham, B.S.Kanekiyo, M.

(2022) Immunity 55: 2405-2418.e7

  • DOI: https://doi.org/10.1016/j.immuni.2022.10.015
  • Primary Citation of Related Structures:  
    6XSK

  • PubMed Abstract: 

    Current influenza vaccines predominantly induce immunity to the hypervariable hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, the immunosubdominant yet conserved HA stem harbors a supersite that is targeted by broadly neutralizing antibodies (bnAbs), representing a prime target for universal vaccines. Here, we showed that the co-immunization of two HA stem immunogens derived from group 1 and 2 influenza A viruses elicits cross-group protective immunity and neutralizing antibody responses in mice, ferrets, and nonhuman primates (NHPs). Immunized mice were protected from multiple group 1 and 2 viruses, and all animal models showed broad serum-neutralizing activity. A bnAb isolated from an immunized NHP broadly neutralized and protected against diverse viruses, including H5N1 and H7N9. Genetic and structural analyses revealed strong homology between macaque and human bnAbs, illustrating common biophysical constraints for acquiring cross-group specificity. Vaccine elicitation of stem-directed cross-group-protective immunity represents a step toward the development of broadly protective influenza vaccines.


  • 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
789-203-3C12 Fab Light ChainA [auth L],
I [auth J],
K
214Macaca mulattaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
789-203-3C12 Fab Heavy ChainB [auth H],
J [auth G],
L [auth I]
455Macaca mulattaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainC [auth A],
E [auth C],
G [auth E]
343Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus)
Explore A7Y8I1 
Go to UniProtKB:  A7Y8I1
Entity Groups  
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UniProt GroupA7Y8I1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainD [auth B],
F [auth D],
H [auth F]
222Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus)
Explore A7Y8I1 
Go to UniProtKB:  A7Y8I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7Y8I1
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, Q, T
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N, O, P, R, S
N, O, P, R, S, U
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth D]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth D],
FA [auth E],
GA [auth E],
HA [auth E],
IA [auth E],
JA [auth F],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--
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: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Source and taxonomy, Structure summary
  • Version 1.2: 2021-09-22
    Changes: Database references, Structure summary
  • Version 1.3: 2023-02-01
    Changes: Database references, Refinement description