2XA3

crystal structure of the broadly neutralizing llama VHH D7 and its mode of HIV-1 gp120 interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the neutralizing Llama V(HH) D7 and its mode of HIV-1 gp120 interaction.

Hinz, A.Lutje Hulsik, D.Forsman, A.Koh, W.W.Belrhali, H.Gorlani, A.de Haard, H.Weiss, R.A.Verrips, T.Weissenhorn, W.

(2010) PLoS ONE 5: e10482-e10482

  • DOI: 10.1371/journal.pone.0010482

  • PubMed Abstract: 
  • HIV-1 entry into host cells is mediated by the sequential binding of the envelope glycoprotein gp120 to CD4 and a chemokine receptor. Antibodies binding to epitopes overlapping the CD4-binding site on gp120 are potent inhibitors of HIV entry, such as ...

    HIV-1 entry into host cells is mediated by the sequential binding of the envelope glycoprotein gp120 to CD4 and a chemokine receptor. Antibodies binding to epitopes overlapping the CD4-binding site on gp120 are potent inhibitors of HIV entry, such as the llama heavy chain antibody fragment V(HH) D7, which has cross-clade neutralizing properties and competes with CD4 and mAb b12 for high affinity binding to gp120. We report the crystal structure of the D7 V(HH) at 1.5 A resolution, which reveals the molecular details of the complementarity determining regions (CDR) and substantial flexibility of CDR3 that could facilitate an induced fit interaction with gp120. Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction. Mutational analysis identified CDR3 as a key component of gp120 interaction as determined by surface plasmon resonance. A decrease in affinity is directly coupled to the neutralization efficiency since mutations that decrease gp120 interaction increase the IC50 required for HIV-1 IIIB neutralization. Thus the structural study identifies the long CDR3 of D7 as the key determinant of interaction and HIV-1 neutralization. Furthermore, our data confirm that the structural plasticity of gp120 can accommodate multiple modes of antibody binding within the CD4 binding site.


    Related Citations: 
    • Llama Antibody Fragments with Cross-Subtype Human Immunodeficiency Virus Type 1 (HIV-1)-Neutralizing Properties and High Affinity for HIV-1 Gp120.
      Forsman, A.,Beirnaert, E.,Aasa-Chapman, M.M.I.,Hoorelbeke, B.,Hijazi, K.,Koh, W.,Tack, V.,Szynol, A.,Kelly, C.,Mcknight, A.,Verrips, T.,De Haard, H.,Weiss, R.A.
      (2008) J.Virol. 82: 12069


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LLAMA HEAVY CHAIN ANTIBODY D7
A
127N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.370α = 90.00
b = 62.180β = 90.00
c = 62.740γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-07
    Type: Database references, Source and taxonomy, Structure summary