1YC7 | pdb_00001yc7

cAbAn33 VHH fragment against VSG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.212 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1YC7

This is version 1.3 of the entry. See complete history

Literature

Antigen Binding and Solubility Effects upon the Veneering of a Camel VHH in Framework-2 to Mimic a VH.

Conrath, K.Vincke, C.Stijlemans, B.Schymkowitz, J.Decanniere, K.Wyns, L.Muyldermans, S.Loris, R.

(2005) J Mol Biology 350: 112-125

  • DOI: https://doi.org/10.1016/j.jmb.2005.04.050
  • Primary Citation Related Structures: 
    1YC7, 1YC8, 1YZZ

  • PubMed Abstract: 

    Heavy chain only antibodies of camelids bind their antigens with a single domain, the VHH, which acquired adaptations relative to classical VHs to function in the absence of a VL partner. Additional CDR loop conformations, outside the canonical loop structures of VHs, broaden the repertoire of the antigen-binding site. The combined effects of part of the CDR3 that folds over the "former" VL binding site and framework-2 mutations to more hydrophilic amino acids, enhance the solubility of VHH domains and prevent VL pairing. cAbAn33, a VHH domain specific for the carbohydrate moiety of the variant surface glycoprotein of trypanosomes, has a short CDR3 loop that does not cover the former VL binding site as well as a VH-specific Trp47 instead of the VHH-specific Gly47. Resurfacing its framework-2 region (mutations Tyr37Val, Glu44Gly and Arg45Leu) to mimic that of a human VH restores the VL binding capacity. In solution, the humanised VHH behaves as a soluble, monomeric entity, albeit with reduced thermodynamic stability and affinity for its antigen. Comparison of the crystal structures of cAbAn33 and its humanised derivative reveals steric hindrance exerted by VHH-specific residues Tyr37 and Arg45 that prevent the VL domain pairing, whereas Glu44 and Arg45 are key elements to avoid insolubility of the domain.


  • Organizational Affiliation
    • Laboratorium voor Cellulaire en Moleculaire Immunologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium. kconrath@vub.ac.be

Macromolecule Content 

  • Total Structure Weight: 27.78 kDa 
  • Atom Count: 2,000 
  • Modeled Residue Count: 232 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-VSG immunoglobulin heavy chain variable domain cAbAn33
A, B
124Camelus dromedariusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.212 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.993α = 90
b = 91.6β = 90
c = 82.409γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary