8UT9

CryoEM structure of A/Shanghai/1/2013 H7 in complex with polyclonal Fab from mice immunized with H7 stem nanoparticles-28 days post immunization


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.

Ray, R.Nait Mohamed, F.A.Maurer, D.P.Huang, J.Alpay, B.A.Ronsard, L.Xie, Z.Han, J.Fernandez-Quintero, M.Phan, Q.A.Ursin, R.L.Vu, M.Kirsch, K.H.Prum, T.Rosado, V.C.Bracamonte-Moreno, T.Okonkwo, V.Bals, J.McCarthy, C.Nair, U.Kanekiyo, M.Ward, A.B.Schmidt, A.G.Batista, F.D.Lingwood, D.

(2024) Immunity 57: 1141-1159.e11

  • DOI: https://doi.org/10.1016/j.immuni.2024.03.022
  • Primary Citation of Related Structures:  
    8UT3, 8UT4, 8UT5, 8UT6, 8UT7, 8UT8, 8UT9, 8UWA

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.


  • Organizational Affiliation

    The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
317Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for V5IRV0 (Influenza A virus)
Explore V5IRV0 
Go to UniProtKB:  V5IRV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5IRV0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
231Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A067Y6L0 (Influenza A virus)
Explore A0A067Y6L0 
Go to UniProtKB:  A0A067Y6L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067Y6L0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H7D28 pFab HC Fv_polyA126Mus musculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H7D28 pFab LC Fv_polyA108Mus musculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79924RM
GlyCosmos:  G79924RM
GlyGen:  G79924RM
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, K
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 
L [auth A]
M [auth A]
N [auth B]
O [auth C]
P [auth C]
L [auth A],
M [auth A],
N [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth E],
S [auth E],
T [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary