4HG4

Crystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

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This is version 2.0 of the entry. See complete history


Literature

A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.

Xu, R.Krause, J.C.McBride, R.Paulson, J.C.Crowe, J.E.Wilson, I.A.

(2013) Nat Struct Mol Biol 20: 363-370

  • DOI: https://doi.org/10.1038/nsmb.2500
  • Primary Citation of Related Structures:  
    4HF5, 4HFU, 4HG4

  • PubMed Abstract: 

    Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold to obtain broad, potent HA inhibitors. Here, we report crystal structures of Fab fragments from three human antibodies that neutralize the 1957 pandemic H2N2 influenza virus in complex with H2 HA. All three antibodies use an aromatic residue to plug a conserved cavity in the HA receptor-binding site. Each antibody interacts with the absolutely conserved HA1 Trp153 at the cavity base through π-π stacking with the signature Phe54 of two VH1-69-encoded antibodies or a tyrosine from HCDR3 in the other antibody. This highly conserved interaction can be used as a starting point to design inhibitors targeting this conserved hydrophobic pocket in influenza viruses.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1327Influenza A virus (A/Japan/305+/1957(H2N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03451 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Explore P03451 
Go to UniProtKB:  P03451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03451
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2174Influenza A virus (A/Japan/305+/1957(H2N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03451 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Explore P03451 
Go to UniProtKB:  P03451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03451
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 2G1 heavy chain223Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 2G1 light chain214Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
KA [auth j],
LA [auth k],
NA [auth m],
OA [auth n],
PA [auth o],
KA [auth j],
LA [auth k],
NA [auth m],
OA [auth n],
PA [auth o],
RA [auth q],
SA [auth r],
TA [auth s],
UA [auth t]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseMA [auth l],
QA [auth p]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.842α = 90
b = 133.143β = 90
c = 812.99γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary