2XRA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 

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

  • 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 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 Ã… 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSMEMBRANE PROTEIN GP41
A
228Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HK20, HUMAN MONOCLONAL ANTIBODY HEAVY CHAIN
H
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HK20, HUMAN MONOCLONAL ANTIBODY LIGHT CHAIN
L
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.947α = 90.00
b = 62.710β = 97.70
c = 76.610γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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