6E56

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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, Duke University, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA. Electronic address: ghkelsoe@duke.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HemagglutininA, D290Influenza A virus (A/Aichi/2/1968(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Explore P03437 
Go to UniProtKB:  P03437
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody H2214 heavy chainG, H253Homo sapiensMutation(s): 0 
Gene Names: IGHV3-23*01
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody H2214 light chain, K1642I, J215Homo sapiensMutation(s): 0 
Gene Names: IGKV3-15*01
Find proteins for Q6PIL8 (Homo sapiens)
Explore Q6PIL8 
Go to UniProtKB:  Q6PIL8
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.55α = 90
b = 98.71β = 90
c = 224.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI089618
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1U19AI117892-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI128832

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary