5GJS

Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

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This is version 2.0 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:  
    5GJS, 5GJT

  • 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 report that a V H 4-4-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 ...

    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 V H 4-4-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

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA329Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 2 
Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S1 
Go to UniProtKB:  C3W5S1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB182Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S1 
Go to UniProtKB:  C3W5S1
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
light chain of human neutralizing antibody 3E1C [auth L]214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
heavy chain of human neutralizing antibody 3E1D [auth H]222Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.162α = 90
b = 130.162β = 90
c = 365.853γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary