6II8

Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L4B-18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-function analysis of neutralizing antibodies to H7N9 influenza from naturally infected humans.

Huang, K.A.Rijal, P.Jiang, H.Wang, B.Schimanski, L.Dong, T.Liu, Y.M.Chang, P.Iqbal, M.Wang, M.C.Chen, Z.Song, R.Huang, C.C.Yang, J.H.Qi, J.Lin, T.Y.Li, A.Powell, T.J.Jan, J.T.Ma, C.Gao, G.F.Shi, Y.Townsend, A.R.

(2019) Nat Microbiol 4: 306-315

  • DOI: 10.1038/s41564-018-0303-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Little is known about the specificities and neutralization breadth of the H7-reactive antibody repertoire induced by natural H7N9 infection in humans. We have isolated and characterized 73 H7-reactive monoclonal antibodies from peripheral B cells fro ...

    Little is known about the specificities and neutralization breadth of the H7-reactive antibody repertoire induced by natural H7N9 infection in humans. We have isolated and characterized 73 H7-reactive monoclonal antibodies from peripheral B cells from four donors infected in 2013 and 2014. Of these, 45 antibodies were H7-specific, and 17 of these neutralized the virus, albeit with few somatic mutations in their variable domain sequences. An additional set of 28 antibodies, isolated from younger donors born after 1968, cross-reacted between H7 and H3 haemagglutinins in binding assays, and had accumulated significantly more somatic mutations, but were predominantly non-neutralizing in vitro. Crystal structures of three neutralizing and protective antibodies in complex with the H7 haemagglutinin revealed that they recognize overlapping residues surrounding the receptor-binding site of haemagglutinin. One of the antibodies, L4A-14, bound into the sialic acid binding site and made contacts with haemagglutinin residues that were conserved in the great majority of 2016-2017 H7N9 isolates. However, only 3 of the 17 neutralizing antibodies retained activity for the Yangtze River Delta lineage viruses isolated in 2016-2017 that have undergone antigenic change, which emphasizes the need for updated H7N9 vaccines.


    Organizational Affiliation

    Department of Cardiovascular Surgery, Min-Sheng General Hospital, Taoyuan, Taiwan.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. shiyi@im.ac.cn.,Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. gaof@im.ac.cn.,Center for translational Immunology, Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK. alain.townsend@imm.ox.ac.uk.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. gaof@im.ac.cn.,Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. shiyi@im.ac.cn.,School of Medicine, Chang Gung University, Taoyuan, Taiwan. arthur1726@cgmh.org.tw.,Clinical and Research Center of Infectious Diseases, The National Clinical Key Department of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK. alain.townsend@imm.ox.ac.uk.,Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Center for translational Immunology, Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK.,Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.,College of Veterinary Medicine, China Agricultural University, Beijing, China.,The Pirbright Institute, Pirbright, Woking, UK.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan. arthur1726@cgmh.org.tw.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A, C, E
316Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for A0A024CX39 (Influenza A virus)
Go to UniProtKB:  A0A024CX39
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B, D, F
172Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for A0A0K1LUI9 (Influenza A virus)
Go to UniProtKB:  A0A0K1LUI9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of L4B-18 Fab
J, G, H
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Light chain of L4B-18 Fab
K, I, L
213N/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, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 203.409α = 90.00
b = 116.062β = 108.99
c = 185.207γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81621091
National Natural Science Foundation of ChinaChina81622031
Chinese Academy of SciencesChinaXDB29010000

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references
  • Version 1.2: 2019-02-06
    Type: Data collection, Database references