NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex

Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1397-404. doi: 10.1107/s0907444901012434. Epub 2001 Sep 21.


Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.

Publication types

  • Comparative Study

MeSH terms

  • Bacterial Proteins / chemistry*
  • Colicins*
  • Crystallography, X-Ray*
  • Humans
  • Magnetic Resonance Spectroscopy*
  • Models, Molecular*
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism
  • Phosphatidylinositol 3-Kinases / chemistry*
  • Phosphatidylinositol 3-Kinases / metabolism
  • Protein Conformation
  • Receptors, Platelet-Derived Growth Factor / chemistry
  • src Homology Domains


  • Bacterial Proteins
  • Colicins
  • Peptide Fragments
  • colicin immunity proteins
  • Phosphatidylinositol 3-Kinases
  • Receptors, Platelet-Derived Growth Factor