1JTO

Degenerate interfaces in antigen-antibody complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Degenerate interfaces in antigen-antibody complexes.

Decanniere, K.Transue, T.R.Desmyter, A.Maes, D.Muyldermans, S.Wyns, L.

(2001) J Mol Biol 313: 473-478

  • DOI: 10.1006/jmbi.2001.5075
  • Primary Citation of Related Structures:  
    1JTP, 1JTO, 1JTT

  • PubMed Abstract: 
  • In most of the work dealing with the analysis of protein-protein interfaces, a single X-ray structure is available or selected, and implicitly it is assumed that this structure corresponds to the optimal complex for this pair of proteins. However, we ...

    In most of the work dealing with the analysis of protein-protein interfaces, a single X-ray structure is available or selected, and implicitly it is assumed that this structure corresponds to the optimal complex for this pair of proteins. However, we have found a degenerate interface in a high-affinity antibody-antigen complex: the two independent complexes of the camel variable domain antibody fragment cAb-Lys3 and its antigen hen egg white lysozyme present in the asymmetric unit of our crystals show a difference in relative orientation between antibody and antigen, leading to important differences at the protein-protein interface. A third cAb-Lys3-hen lysozyme complex in a different crystal form adopts yet another relative orientation. Our results show that protein-protein interface characteristics can vary significantly between different specimens of the same high-affinity antibody-protein antigen complex. Consideration should be given to this type of observation when trying to establish general protein-protein interface characteristics.


    Related Citations: 
    • Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme
      Desmyter, A., Transue, T.R., Ghahroudi, M.A., Thi, M.H., Poortmans, F., Hamers, R., Muyldermans, S., Wyns, L.
      (1996) Nat Struct Biol 3: 803

    Organizational Affiliation

    Vrije Universiteit Brussel Dienst Ultrastructuur, Vlaams Instituut voor Biotechnologie, Paardenstraat 65, B-1640 St.-Genesius Rode, Belgium. klaas@ultr.vub.ac.be



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vh Single-Domain AntibodyAB148Camelus dromedariusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LysozymeLM129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.68α = 90
b = 69.71β = 90
c = 113.68γ = 90
Software Package:
Software NamePurpose
Enrafdata collection
SCALAdata scaling
AMoREphasing
CNSrefinement
ENRAFdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection