PDBsum entry 5mfc

De novo protein

PDB id: 5mfc

Contents

Protein chains

285 a.a.

241 a.a.

Ligands

ACT

Waters ×78

PDB id:

5mfc

Name:

De novo protein

Title:

Designed armadillo repeat protein yiiim5aii in complex with (kr)4-gfp

Structure:

Yiiim5aii. Chain: a, c. Engineered: yes. (Kr)4-green fluorescent protein,green fluorescent protein. Chain: b, d. Engineered: yes

Source:

Synthetic construct. Organism_taxid: 32630. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Aequorea victoria. Jellyfish. Organism_taxid: 6100. Gene: gfp. Expression_system_taxid: 83333

Resolution:

2.40Å R-factor: 0.219 R-free: 0.240

Authors:

S.Hansen,J.Kiefer,C.Madhurantakam,P.Mittl,A.Plueckthun

Key ref:

S.Hansen et al. (2017). Structures of designed armadillo repeat proteins binding to peptides fused to globular domains. Protein Sci, 26, 1942-1952. PubMed id: 28691351

Date:

18-Nov-16 Release date: 19-Jul-17

Protein chains

No UniProt id for this chain

Struc: 285 a.a.

Protein chains

A0A059PIQ0  (A0A059PIQ0_AEQVI) -  Green fluorescent protein (Fragment) from Aequorea victoria

Seq: 251 a.a.

Struc: 241 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Protein Sci 26:1942-1952 (2017)

PubMed id: 28691351

Structures of designed armadillo repeat proteins binding to peptides fused to globular domains.

S.Hansen, J.D.Kiefer, C.Madhurantakam, P.R.E.Mittl, A.Plückthun.

ABSTRACT

Designed armadillo repeat proteins (dArmRP) are α-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D. These structures demonstrate that dArmRPs bind unfolded peptides in the intended conformation also when they constitute unstructured parts of folded proteins, which greatly expands possible applications of the dArmRP technology. Nonetheless, the structures do not fully reflect the binding behavior in solution, that is, some binding sites remain unoccupied in the crystal and even unexpected peptide residues appear to be bound. We show how these differences can be explained by restrictions of the crystal lattice or the composition of the crystallization solution. This illustrates that crystal structures have to be interpreted with caution when protein-peptide interactions are characterized, and should always be correlated with measurements in solution.