6II9

Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L3A-44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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This is version 1.3 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: https://doi.org/10.1038/s41564-018-0303-7
  • Primary Citation of Related Structures:  
    6II4, 6II8, 6II9

  • 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 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

    Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan. arthur1726@cgmh.org.tw.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
A, C, E
317Influenza A virus (A/Anhui/DEWH72-02/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A024CX39 (Influenza A virus)
Explore A0A024CX39 
Go to UniProtKB:  A0A024CX39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024CX39
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
B, D, F
170Influenza A virus (A/Anhui/1-YK_RG123/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0K1LUI9 (Influenza A virus)
Explore A0A0K1LUI9 
Go to UniProtKB:  A0A0K1LUI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1LUI9
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of L3A-44 FabG [auth H],
I [auth M],
K [auth P]
221Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of L3A-44 FabH [auth L],
J [auth N],
L [auth Q]
212Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.457α = 90
b = 184.906β = 106.47
c = 188.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary