4HF5

Crystal structure of Fab 8F8 in complex a H2N2 influenza virus hemagglutinin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.

Xu, R., Krause, J.C., McBride, R., Paulson, J.C., Crowe, J.E., Wilson, I.A.

(2013) Nat.Struct.Mol.Biol. 20: 363-370

  • DOI: 10.1038/nsmb.2500
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold ...

    Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold to obtain broad, potent HA inhibitors. Here, we report crystal structures of Fab fragments from three human antibodies that neutralize the 1957 pandemic H2N2 influenza virus in complex with H2 HA. All three antibodies use an aromatic residue to plug a conserved cavity in the HA receptor-binding site. Each antibody interacts with the absolutely conserved HA1 Trp153 at the cavity base through π-π stacking with the signature Phe54 of two VH1-69-encoded antibodies or a tyrosine from HCDR3 in the other antibody. This highly conserved interaction can be used as a starting point to design inhibitors targeting this conserved hydrophobic pocket in influenza viruses.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1
A
327Influenza A virus (strain A/Japan/305/1957 H2N2)Mutation(s): 0 
Gene Names: HA
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Go to UniProtKB:  C7S226
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2
B
174Influenza A virus (strain A/Japan/305/1957 H2N2)Mutation(s): 0 
Gene Names: HA
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Go to UniProtKB:  C7S226
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab 8F8 heavy chain
H
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab 8F8 light chain
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.615α = 90.00
b = 136.615β = 90.00
c = 142.134γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-10-04 
  • Released Date: 2013-02-13 
  • Deposition Author(s): Xu, R., Wilson, I.A.

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description