9B2M | pdb_00009b2m

Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9B2M

This is version 1.0 of the entry. See complete history

Literature

Modulating the immunodominance hierarchy of immunoglobulin germline-encoded structural motifs targeting the influenza hemagglutinin stem.

Ataca, S.Sangesland, M.de Paiva Froes Rocha, R.Torrents de la Pena, A.Ronsard, L.Boyoglu-Barnum, S.Gillespie, R.A.Tsybovsky, Y.Stephens, T.Moin, S.M.Lederhofer, J.Creanga, A.Andrews, S.F.Barnes, R.M.Rohrer, D.Lonberg, N.Graham, B.S.Ward, A.B.Lingwood, D.Kanekiyo, M.

(2024) Cell Rep 43: 114990-114990

  • DOI: https://doi.org/10.1016/j.celrep.2024.114990
  • Primary Citation Related Structures: 
    9B2M

  • PubMed Abstract: 

    Antibodies targeting epitopes through germline-encoded motifs can be found in different individuals. While these public antibodies are often beneficial, they also pose hurdles for subdominant antibodies to emerge. Here, we use transgenic mice that reproduce the human IGHV1-69 01 germline-encoded antibody response to the conserved stem epitope on group 1 hemagglutinin (HA) of influenza A virus to show that this germline-endowed response can be overridden by a subdominant yet cross-group reactive public antibody response. Immunization with a non-cognate group 2 HA stem enriched B cells harboring the IGHD3-9 gene, thereby switching from IGHV1-69- to IGHD3-9-encoded motif-dependent epitope recognition. These IGHD3-9 antibodies bound, neutralized, and conferred cross-group protection in mice against influenza A viruses. A cryoelectron microscopy (cryo-EM) structure of an IGHD3-9 antibody resembled the human broadly neutralizing antibody FI6v3, which uses IGHD3-9. Together, our findings offer insights into vaccine regimens that engage an immunoglobulin repertoire with broader cross-reactivity to influenza A viruses.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 340.23 kDa 
  • Atom Count: 17,412 
  • Modeled Residue Count: 2,187 
  • Deposited Residue Count: 3,054 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA [auth C],
E [auth A],
I [auth G]
339Influenza 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
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainB [auth D],
F [auth B],
J [auth I]
226Influenza 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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain monoclonal antibody Fab 3_S0008C [auth H],
G [auth E],
K [auth J]
233Mus sp.Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain monoclonal antibody Fab 3_S0008D [auth L],
H [auth F],
L [auth K]
220Mus sp.Mutation(s): 0 

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 G]
M [auth C]
N [auth C]
O [auth C]
P [auth C]
AA [auth G],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth G],
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: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTRosettaEM

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1170236
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release