4LVH

Insight into highly conserved H1 subtype-specific epitopes in influenza virus hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insight into highly conserved h1 subtype-specific epitopes in influenza virus hemagglutinin

Cho, K.J.Hong, K.W.Kim, S.H.Seok, J.H.Kim, S.Lee, J.-H.Saelens, X.Kim, K.H.

(2014) Plos One 9: e89803-e89803

  • DOI: 10.1371/journal.pone.0089803

  • PubMed Abstract: 
  • Influenza viruses continuously undergo antigenic changes with gradual accumulation of mutations in hemagglutinin (HA) that is a major determinant in subtype specificity. The identification of conserved epitopes within specific HA subtypes gives an im ...

    Influenza viruses continuously undergo antigenic changes with gradual accumulation of mutations in hemagglutinin (HA) that is a major determinant in subtype specificity. The identification of conserved epitopes within specific HA subtypes gives an important clue for developing new vaccines and diagnostics. We produced and characterized nine monoclonal antibodies that showed significant neutralizing activities against H1 subtype influenza viruses, and determined the complex structure of HA derived from a 2009 pandemic virus A/Korea/01/2009 (KR01) and the Fab fragment from H1-specific monoclonal antibody GC0587. The overall structure of the complex was essentially identical to the previously determined KR01 HA-Fab0757 complex structure. Both Fab0587 and Fab0757 recognize readily accessible head regions of HA, revealing broadly shared and conserved antigenic determinants among H1 subtypes. The β-strands constituted by Ser110-Glu115 and Lys169-Lys170 form H1 epitopes with distinct conformations from those of H1 and H3 HA sites. In particular, Glu112, Glu115, Lys169, and Lys171 that are highly conserved among H1 subtype HAs have close contacts with HCDR3 and LCDR3. The differences between Fab0587 and Fab0757 complexes reside mainly in HCDR3 and LCDR3, providing distinct antigenic determinants specific for 1918 pdm influenza strain. Our results demonstrate a potential key neutralizing epitope important for H1 subtype specificity in influenza virus.


    Organizational Affiliation

    Antibody Engineering Laboratory, Central Research Center, Green Cross Corp., Yongin Kyunggi, Korea.,Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea.,VIB Inflammation Research Center, Ghent, Belgium ; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A, D, G, J
518Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for C5MQE6 (Influenza A virus)
Go to UniProtKB:  C5MQE6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MONOCLONAL ANTIBODY H-CHAIN
B, E, H, K
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MONOCLONAL ANTIBODY L-CHAIN
C, F, I, L
211N/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
CA
Query on CA

Download SDF File 
Download CCD File 
A, D, G, J
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.751α = 90.00
b = 237.814β = 110.31
c = 94.230γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description