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Mol Cells. 2019 Oct 31;42(10):729-738. doi: 10.14348/molcells.2019.0096.

Oligomer Model of PB1 Domain of p62/SQSTM1 Based on Crystal Structure of Homo-Dimer and Calculation of Helical Characteristics.

Author information

1
Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
2
Department of Biochemistry, Chungnam National University, Daejeon 34134, Korea.
3
Department of Biology, Chungnam National University, Daejeon 34134, Korea.

Abstract

Autophagy is an important process for protein recycling. Oligomerization of p62/SQSTM1 is an essential step in this process and is achieved in two steps. Phox and Bem1p (PB1) domains can oligomerize through both basic and acidic surfaces in each molecule. The ZZ-type zinc finger (ZZ) domain binds to target proteins and promotes higheroligomerization of p62. This mechanism is an important step in routing target proteins to the autophagosome. Here, we determined the crystal structure of the PB1 homo-dimer and modeled the p62 PB1 oligomers. These oligomer models were represented by a cylindrical helix and were compared with the previously determined electron microscopic map of a PB1 oligomer. To accurately compare, we mathematically calculated the lead length and radius of the helical oligomers. Our PB1 oligomer model fits the electron microscopy map and is both bendable and stretchable as a flexible helical filament.

KEYWORDS:

Phox and Bem1p; autophagy; calculation; cylindrical helix; helical oligomer; lead length of helix; p62/SQSTM1; pitch of helix; radius of helix

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