6J9O | pdb_00006j9o

Crystal structure of a free scFv molecule from a group 2 influenza A viruses HA binding antibody AF4H1K1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.192 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6J9O

This is version 1.2 of the entry. See complete history

Literature

Light chain modulates heavy chain conformation to change protection profile of monoclonal antibodies against influenza A viruses.

Xiao, H.Guo, T.Yang, M.Qi, J.Huang, C.Hong, Y.Gu, J.Pang, X.Liu, W.J.Peng, R.McCauley, J.Bi, Y.Li, S.Feng, J.Zhang, H.Zhang, X.Lu, X.Yan, J.Chen, L.Shi, Y.Chen, W.Gao, G.F.

(2019) Cell Discov 5: 21-21

  • DOI: https://doi.org/10.1038/s41421-019-0086-x
  • Primary Citation Related Structures: 
    6J9O

  • PubMed Abstract: 

    The isolation of human monoclonal antibodies with broadly neutralizing breadth can provide a promising countermeasure for influenza A viruses infection. Most broadly neutralizing antibodies against influenza A viruses bind to the conserved stem region or the receptor-binding cavity of hemagglutinin and the interaction is dominated by the heavy chain. The light chain, however, contributes few or no direct contacts to the antigen. Here we report an H3-clade neutralizing human monoclonal antibody, AF4H1K1, which recognizes the hemagglutinin glycoproteins of all group 2 influenza A viruses. This human monoclonal antibody has been obtained through the screening by pairing different heavy and light chains from an H7N9-infected patient based on the next-generation sequencing technology. Further structural studies revealed that light chains modulate the neutralizing spectrum by affecting the local conformation of heavy chains, instead of direct interaction with the antigen. These findings provide important clues to understand the molecular basis of light chains in antigen recognition and to explore the strategies in particular of the use of light chain modification to develop broadly protective monoclonal antibodies against influenza A viruses and other emerging viruses.


  • Organizational Affiliation
    • 1Laboraroty of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences (CAS), Tianjin, 300308 China.

Macromolecule Content 

  • Total Structure Weight: 26.09 kDa 
  • Atom Count: 2,148 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 238 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of AF4H1K1 scFvA [auth H]130Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of AF4H1K1 scFvB [auth L]108Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.192 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.747α = 90
b = 56.798β = 90
c = 102.581γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary