4M4Y

Crystal structure of a 2009 H1N1 influenza virus hemagglutinin with a stabilization mutation HA2 E47G

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site.

Hong, M., Lee, P.S., Hoffman, R.M., Zhu, X., Krause, J.C., Laursen, N.S., Yoon, S.I., Song, L., Tussey, L., Crowe, J.E., Ward, A.B., Wilson, I.A.

(2013) J.Virol. 87: 12471-12480

  • DOI: 10.1128/JVI.01388-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 ...

    Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918 and 2009 pandemic viruses. Here, we present the crystal structure of 5J8 Fab in complex with a bacterially expressed and refolded globular head domain from the hemagglutinin (HA) of the A/California/07/2009 (H1N1) pandemic virus. 5J8 recognizes a conserved epitope in and around the receptor binding site (RBS), and its HCDR3 closely mimics interactions of the sialic acid receptor. Electron microscopy (EM) reconstructions of 5J8 Fab in complex with an HA trimer from a 1986 H1 strain and with an engineered stabilized HA trimer from the 2009 H1 pandemic virus showed a similar mode of binding. As for other characterized RBS-targeted antibodies, 5J8 uses avidity to extend its breadth and affinity against divergent H1 strains. 5J8 selectively interacts with HA insertion residue 133a, which is conserved in pandemic H1 strains and has precluded binding of other RBS-targeted antibodies. Thus, the RBS of divergent HAs is targeted by 5J8 and adds to the growing arsenal of common recognition motifs for design of therapeutics and vaccines. Moreover, consistent with previous studies, the bacterially expressed H1 HA properly refolds, retaining its antigenic structure, and presents a low-cost and rapid alternative for engineering and manufacturing candidate flu vaccines.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 subunit
A, C, E
331Influenza A virus (strain swl A/California/04/2009 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Go to UniProtKB:  C3W5S1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 subunit
B, D, F
177Influenza A virus (strain swl A/California/04/2009 H1N1)Mutation(s): 1 
Gene Names: HA
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Go to UniProtKB:  C3W5S1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download SDF File 
Download CCD File 
C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL
Download SDF File 
Download CCD File 
E
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.367α = 90.00
b = 132.174β = 90.00
c = 201.809γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2013-08-07 
  • Released Date: 2013-09-25 
  • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Database references