5GJT

Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human antibody 3E1 targets the HA stem region of H1N1 and H5N6 influenza A viruses

Wang, W.Sun, X.Li, Y.Su, J.Ling, Z.Zhang, T.Wang, F.Zhang, H.Chen, H.Ding, J.Sun, B.

(2016) Nat Commun 7: 13577-13577

  • DOI: 10.1038/ncomms13577
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As influenza A viruses remain a major threat to human health worldwide, the discovery of broadly neutralizing monoclonal antibodies that recognize conserved epitopes would facilitate the development of antibody-based therapeutic strategies. Here we r ...

    As influenza A viruses remain a major threat to human health worldwide, the discovery of broadly neutralizing monoclonal antibodies that recognize conserved epitopes would facilitate the development of antibody-based therapeutic strategies. Here we report that a VH4-4-encoded human mAb named 3E1 could neutralize H1 and H5 subtype viruses in vitro and protect mice against the H1N1 and H5N6 viruses by inhibiting the low pH-induced conformational rearrangement of haemagglutinin (HA), hence blocking membrane fusion. The crystal structures of 3E1 Fab in complex with HA of two H1N1 strains reveal that 3E1, with both heavy and light chains, binds to a conserved epitope of the HA stem region, comprising parts of the fusion peptide, the F subdomain and the outermost β-strand preceding helix A. Altogether, these data suggest the potential of 3E1 as a therapeutic drug against H1 and H5 subtype viruses.


    Organizational Affiliation

    National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
329Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for N0C8E5 (Influenza A virus)
Go to UniProtKB:  N0C8E5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B
182Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for N0C8E5 (Influenza A virus)
Go to UniProtKB:  N0C8E5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
light chain of human neutralizing antibody 3E1
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
heavy chain of human neutralizing antibody 3E1
H
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 3.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 130.806α = 90.00
b = 130.806β = 90.00
c = 366.938γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Source and taxonomy