4XNQ

Antibody hemagglutinin Complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Vaccine-elicited antibody that neutralizes H5N1 influenza and variants binds the receptor site and polymorphic sites.

Winarski, K.L.Thornburg, N.J.Yu, Y.Sapparapu, G.Crowe, J.E.Spiller, B.W.

(2015) Proc.Natl.Acad.Sci.USA 112: 9346-9351

  • DOI: 10.1073/pnas.1502762112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antigenic drift of circulating seasonal influenza viruses necessitates an international vaccine effort to reduce the impact on human health. A critical feature of the seasonal vaccine is that it stimulates an already primed immune system to diversify ...

    Antigenic drift of circulating seasonal influenza viruses necessitates an international vaccine effort to reduce the impact on human health. A critical feature of the seasonal vaccine is that it stimulates an already primed immune system to diversify memory B cells to recognize closely related, but antigenically distinct, influenza glycoproteins (hemagglutinins). Influenza pandemics arise when hemagglutinins to which no preexisting adaptive immunity exists acquire the capacity to infect humans. Hemagglutinin 5 is one subtype to which little preexisting immunity exists and is only a few acquired mutations away from the ability to transmit efficiently between ferrets, and possibly humans. Here, we describe the structure and molecular mechanism of neutralization by H5.3, a vaccine-elicited antibody that neutralizes hemagglutinin 5 viruses and variants with expanded host range. H5.3 binds in the receptor-binding site, forming contacts that recapitulate many of the sialic acid interactions, as well as multiple peripheral interactions, yet is not sensitive to mutations that alter sialic acid binding. H5.3 is highly specific for a subset of H5 strains, and this specificity arises from interactions to the periphery of the receptor-binding site. H5.3 is also extremely potent, despite retaining germ line-like conformational flexibility.


    Related Citations: 
    • to be published
      Spiller, B.W.,Winarski, K.L.,Crowe, J.E.,Thronburg, N.J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H5.3 Light chain
A, L
208N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H5.3 heavy chain
B, H
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Influenza H5 HA head domain VietNam rdt mutations
D, C
212Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 250.400α = 90.00
b = 51.178β = 100.17
c = 127.702γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesHHSN272200900047C
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States5R21 AI092268

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Non-polymer description
  • Version 1.2: 2015-07-29
    Type: Database references
  • Version 1.3: 2015-08-12
    Type: Database references
  • Version 1.4: 2015-09-09
    Type: Source and taxonomy
  • Version 1.5: 2017-09-13
    Type: Author supporting evidence, Derived calculations