3RFS: Design Of A Binding Scaffold Based On Variable Lymphocyte Receptors Of Jawless Vertebrates By Module Engineering

Repeat proteins have recently been of great interest as potential alternatives to immunoglobulin antibodies due to their unique structural and biophysical features. We here present the development of a binding scaffold based on variable lymphocyte receptors, which are nonimmunoglobulin antibodies composed of Leucine-rich repeat modules in jawless vertebrates, by module engineering. A template scaffold was first constructed by joining consensus repeat modules between the N- and C-capping motifs of variable lymphocyte receptors. The N-terminal domain of the template scaffold was redesigned based on the internalin-B cap by analyzing the modular similarity between the respective repeat units using a computational approach. The newly designed scaffold, termed "Repebody," showed a high level of soluble expression in bacteria, displaying high thermodynamic and pH stabilities. Ease of molecular engineering was shown by designing repebodies specific for myeloid differentiation protein-2 and hen egg lysozyme, respectively, by a rational approach. The crystal structures of designed repebodies were determined to elucidate the structural features and interaction interfaces. We demonstrate general applicability of the scaffold by selecting repebodies with different binding affinities for interleukin-6 using phage display.
PDB ID: 3RFSDownload
MMDB ID: 97919
PDB Deposition Date: 2011/4/6
Updated in MMDB: 2017/08
Experimental Method:
x-ray diffraction
Resolution: 1.7  Å
Similar Structures:
Biological Unit for 3RFS: monomeric; determined by author and by software (PISA)
Molecular Components in 3RFS
Label Count Molecule
Protein (1 molecule)
Internalin B, Repeat Modules, Variable Lymphocyte Receptor B
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB