4V3Q

Designed armadillo repeat protein with 4 internal repeats, 2nd generation C-cap and 3rd generation N-cap.

Summary for 4V3Q

• Entry DOI: 10.2210/pdb4v3q/pdb
• Related: 4V3O 4V3R
• Descriptor: YIII_M4_AII, GLYCEROL, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: de novo protein, protein engineering, repeat protein, armadillo repeat
• Biological source: SYNTHETIC CONSTRUCT
• Total number of polymer chains: 4
• Total formula weight: 105793.90

Authors

Reichen, C.,Madhurantakam, C.,Pluckthun, A.,Mittl, P. (deposition date: 2014-10-20, release date: 2016-01-13, Last modification date: 2024-01-10)

Primary citation

Reichen, C.,Madhurantakam, C.,Hansen, S.,Grutter, M.G.,Pluckthun, A.,Mittl, P.R.
Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects.
Acta Crystallogr D Struct Biol, 72:168-175, 2016

PubMed Abstract: The armadillo repeat serves as a scaffold for the development of modular peptide-recognition modules. In order to develop such a system, three crystal structures of designed armadillo-repeat proteins with third-generation N-caps (YIII-type), four or five internal repeats (M-type) and second-generation C-caps (AII-type) were determined at 1.8 Å (His-YIIIM4AII), 2.0 Å (His-YIIIM5AII) and 1.95 Å (YIIIM5AII) resolution and compared with those of variants with third-generation C-caps. All constructs are full consensus designs in which the internal repeats have exactly the same sequence, and hence identical conformations of the internal repeats are expected. The N-cap and internal repeats M1 to M3 are indeed extremely similar, but the comparison reveals structural differences in internal repeats M4 and M5 and the C-cap. These differences are caused by long-range effects of the C-cap, contacting molecules in the crystal, and the intrinsic design of the repeat. Unfortunately, the rigid-body movement of the C-terminal part impairs the regular arrangement of internal repeats that forms the putative peptide-binding site. The second-generation C-cap improves the packing of buried residues and thereby the stability of the protein. These considerations are useful for future improvements of an armadillo-repeat-based peptide-recognition system.

PubMed: 26894544
DOI: 10.1107/S2059798315023116

Experimental method

X-RAY DIFFRACTION (1.8 Å)