PDBsum entry 4v3q

De novo protein

PDB id: 4v3q

Contents

Protein chains

247 a.a.

Ligands

GOL ×2

Metals

_CA ×16

Waters ×654

PDB id:

4v3q

Name:

De novo protein

Title:

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

Structure:

Yiii_m4_aii. Chain: a, b, c, d. Engineered: yes

Source:

Synthetic construct. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.192 R-free: 0.236

Authors:

C.Reichen,C.Madhurantakam,A.Pluckthun,P.Mittl

Key ref:

C.Reichen et al. (2016). Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects. Acta Crystallogr D Struct Biol, 72, 168-175. PubMed id: 26894544 DOI: 10.1107/S2059798315023116

Date:

20-Oct-14 Release date: 13-Jan-16

Protein chains

No UniProt id for this chain

Struc: 247 a.a.

DOI no: 10.1107/S2059798315023116

Acta Crystallogr D Struct Biol 72:168-175 (2016)

PubMed id: 26894544

Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects.

C.Reichen, C.Madhurantakam, S.Hansen, M.G.Grütter, A.Plückthun, P.R.Mittl.

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.