2XRA

crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

Sabin, C.Corti, D.Buzon, V.Seaman, M.S.Lutje Hulsik, D.Hinz, A.Vanzetta, F.Agatic, G.Silacci, C.Mainetti, L.Scarlatti, G.Sallusto, F.Weiss, R.Lanzavecchia, A.Weissenhorn, W.

(2010) PLoS Pathog 6: e1001195-e1001195

  • DOI: 10.1371/journal.ppat.1001195
  • Primary Citation of Related Structures:  
    2XRA

  • PubMed Abstract: 
  • The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2 ...

    The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.


    Related Citations: 
    • Structural Basis for HIV-1 Neutralization by a Gp41 Fusion Intermediate-Directed Antibody.
      Luftig, M.A., Mattu, M., Di Giovine, P., Geleziunas, R., Hrin, R., Barbato, G., Bianchi, E., Miller, M.D., Pessi, A., Carfi, A.
      (2006) Nat Struct Mol Biol 13: 740

    Organizational Affiliation

    Unit of Virus Host Cell Interactions, UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSMEMBRANE PROTEIN GP41A228synthetic constructMutation(s): 0 
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HK20, HUMAN MONOCLONAL ANTIBODY HEAVY CHAINB [auth H]223Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HK20, HUMAN MONOCLONAL ANTIBODY LIGHT CHAINC [auth L]215Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.947α = 90
b = 62.71β = 97.7
c = 76.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references, Version format compliance
  • Version 1.2: 2018-02-07
    Changes: Database references, Source and taxonomy, Structure summary