8FJG image
Entry Detail
PDB ID:
8FJG
Keywords:
Title:
The two-repeat design H12
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-12-19
Release Date:
2023-09-27
Method Details:
Experimental Method:
Resolution:
2.13 Å
R-Value Free:
0.27
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:H12
Chain IDs:A
Chain Length:109
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Hallucination of closed repeat proteins containing central pockets.
Nat.Struct.Mol.Biol. 30 1755 1760 (2023)
PMID: 37770718 DOI: 10.1038/s41594-023-01112-6

Abstact

In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.

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