6E56

Human antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibodies to a Conserved Influenza Head Interface Epitope Protect by an IgG Subtype-Dependent Mechanism.

Watanabe, A.McCarthy, K.R.Kuraoka, M.Schmidt, A.G.Adachi, Y.Onodera, T.Tonouchi, K.Caradonna, T.M.Bajic, G.Song, S.McGee, C.E.Sempowski, G.D.Feng, F.Urick, P.Kepler, T.B.Takahashi, Y.Harrison, S.C.Kelsoe, G.

(2019) Cell 177: 1124-1135.e16

  • DOI: 10.1016/j.cell.2019.03.048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vaccines to generate durable humoral immunity against antigenically evolving pathogens such as the influenza virus must elicit antibodies that recognize conserved epitopes. Analysis of single memory B cells from immunized human donors has led us to c ...

    Vaccines to generate durable humoral immunity against antigenically evolving pathogens such as the influenza virus must elicit antibodies that recognize conserved epitopes. Analysis of single memory B cells from immunized human donors has led us to characterize a previously unrecognized epitope of influenza hemagglutinin (HA) that is immunogenic in humans and conserved among influenza subtypes. Structures show that an unrelated antibody from a participant in an experimental infection protocol recognized the epitope as well. IgGs specific for this antigenic determinant do not block viral infection in vitro, but passive administration to mice affords robust IgG subtype-dependent protection against influenza infection. The epitope, occluded in the pre-fusion form of HA, is at the contact surface between HA head domains; reversible molecular "breathing" of the HA trimer can expose the interface to antibody and B cells. Antigens that present this broadly immunogenic HA epitope may be good candidates for inclusion in "universal" flu vaccines.


    Organizational Affiliation

    Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.,Department of Pathology, Duke University, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. Electronic address: harrison@crystal.harvard.edu.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA.,Department of Immunology, Duke University, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA.,Department of Immunology, Duke University, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA. Electronic address: ghkelsoe@duke.edu.,Ragon Institute and Harvard Medical School, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
D, A
290Influenza A virus (strain A/Aichi/2/1968 H3N2)Mutation(s): 0 
Gene Names: HA
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Go to UniProtKB:  P03437
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody H2214 heavy chain
H, G
253N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody H2214 light chain, K1642
I, J
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.550α = 90.00
b = 98.710β = 90.00
c = 224.870γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesP01AI089618
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1U19AI117892-01
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI128832

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references