3WKN

Crystal structure of the artificial protein AFFinger p17 (AF.p17) complexed with Fc fragment of human IgG

Summary for 3WKN

• Entry DOI: 10.2210/pdb3wkn/pdb
• Descriptor: Ig gamma-1 chain C region, AFFinger p17, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: immunoglobulin-like beta-sandwich, binding protein, immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted: P01857
• Total number of polymer chains: 16
• Total formula weight: 253785.25

Authors

Watanabe, H.,Honda, S. (deposition date: 2013-10-29, release date: 2014-10-29, Last modification date: 2024-10-30)

Primary citation

Watanabe, H.,Honda, S.
Adaptive Assembly: Maximizing the Potential of a Given Functional Peptide with a Tailor-Made Protein Scaffold.
Chem.Biol., 22:1165-1173, 2015

PubMed Abstract: Protein engineering that exploits known functional peptides holds great promise for generating novel functional proteins. Here we propose a combinatorial approach, termed adaptive assembly, which provides a tailor-made protein scaffold for a given functional peptide. A combinatorial library was designed to create a tailor-made scaffold, which was generated from β hairpins derived from a 10-residue minimal protein "chignolin" and randomized amino acid sequences. We applied adaptive assembly to a peptide with low affinity for the Fc region of human immunoglobulin G, generating a 54-residue protein AF.p17 with a 40,600-fold enhanced affinity. The crystal structure of AF.p17 complexed with the Fc region revealed that the scaffold fixed the active conformation with a unique structure composed of a short α helix, β hairpins, and a loop-like structure. Adaptive assembly can take full advantage of known peptides as assets for generating novel functional proteins.

PubMed: 26299673
DOI: 10.1016/j.chembiol.2015.07.015

Experimental method

X-RAY DIFFRACTION (2.9 Å)