4HG4

Crystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.249 

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, B, C, D, E, F, G, H, I
327Influenza A virus (strain A/Japan/305/1957 H2N2)Mutation(s): 0 
Gene Names: HA
Find proteins for P03451 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Go to UniProtKB:  P03451
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2
a, b, c, d, e, f, g, h, i
174Influenza A virus (strain A/Japan/305/1957 H2N2)Mutation(s): 0 
Gene Names: HA
Find proteins for P03451 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Go to UniProtKB:  P03451
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab 2G1 heavy chain
J, L, N, P, R, T, V, X, Z
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab 2G1 light chain
K, M, O, Q, S, U, W, Y, z
214N/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
BMA
Query on BMA

Download SDF File 
Download CCD File 
C, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 126.842α = 90.00
b = 133.143β = 90.00
c = 812.990γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-06 
  • 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