1QD0

CAMELID HEAVY CHAIN VARIABLE DOMAINS PROVIDE EFFICIENT COMBINING SITES TO HAPTENS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Camelid heavy-chain variable domains provide efficient combining sites to haptens.

Spinelli, S.Frenken, L.G.Hermans, P.Verrips, T.Brown, K.Tegoni, M.Cambillau, C.

(2000) Biochemistry 39: 1217-1222


  • PubMed Abstract: 
  • Camelids can produce antibodies devoid of light chains and CH1 domains (Hamers-Casterman, C. et al. (1993) Nature 363, 446-448). Camelid heavy-chain variable domains (VHH) have high affinities for protein antigens and the structures of two of these c ...

    Camelids can produce antibodies devoid of light chains and CH1 domains (Hamers-Casterman, C. et al. (1993) Nature 363, 446-448). Camelid heavy-chain variable domains (VHH) have high affinities for protein antigens and the structures of two of these complexes have been determined (Desmyter, A. et al. (1996) Nature Struc. Biol. 3, 803-811; Decanniere, K. et al. (1999) Structure 7, 361-370). However, the small size of these VHHs and their monomeric nature bring into question their capacity to bind haptens. Here, we have successfully raised llama antibodies against the hapten azo-dye Reactive Red (RR6) and determined the crystal structure of the complex between a dimer of this hapten and a VHH fragment. The surface of interaction between the VHH and the dimeric hapten is large, with an area of ca. 300 A(2); this correlates well with the low-dissociation constant of 22 nM measured for the monomer. The VHH fragment provides an efficient combining site to the RR6, using its three CDR loops. In particular, CDR1 provides a strong interaction to the hapten through two histidine residues bound to its copper atoms. VHH fragments might, therefore, prove to be valuable tools for selecting, removing, or capturing haptens. They are likely to play a role in biotechnology extending beyond protein recognition alone.


    Related Citations: 
    • Naturally Occurring Antibodies Devoid of Light Chains
      Hamers-Casterman, C.,Atarhouch, T.,Muyldermans, S.,Robinson, G.,Hamers, C.,Songa, E.B.,Bendahman, N.,Hamers, R.
      (1993) Nature 363: 446


    Organizational Affiliation

    Architecture et Fonction des Macromolecules Biologiques, CNRS, UPR-9039, 31 Chemiin Joseph Aiguier, 13402 Marseille Cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VHH-R2 ANTI-RR6 ANTIBODY
A
128Lama glamaGene Names: r2
Find proteins for A2KD59 (Lama glama)
Go to UniProtKB:  A2KD59
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RR6
Query on RR6

Download SDF File 
Download CCD File 
A
3-HYDROXY-7-(4-{1-[2-HYDROXY-3-(2-HYDROXY-5-SULFO-PHENYLAZO)-BENZYL]-2-SULFO-ETHYLAMINO}-[1,2,5]TRIAZIN-2-YLAMINO)-2-(2-HYDROXY-5-SULFO-PHENYLAZO)-NAPTHALENE-1,8-DISULFONIC ACID
AZO-DYE RR6 HAPTEN
C35 H25 N9 O22 S6
PJONDRDKCIFXDA-CHQNLTHESA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 46.700α = 90.00
b = 46.700β = 90.00
c = 121.100γ = 120.00
Software Package:
Software NamePurpose
AUTOMARdata reduction
X-PLORrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description