Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1

Jianxiu Zhang, Ying-Ying Wang, Zhao-Qian Pan, Yulu Li, Jianhua Sui, Li-Lin Du () and Keqiong Ye ()
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Jianxiu Zhang: Chinese Academy of Sciences
Ying-Ying Wang: Beijing Normal University
Zhao-Qian Pan: National Institute of Biological Sciences
Yulu Li: National Institute of Biological Sciences
Jianhua Sui: National Institute of Biological Sciences
Li-Lin Du: National Institute of Biological Sciences
Keqiong Ye: Chinese Academy of Sciences

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Neighbor of BRCA1 (Nbr1) is a conserved autophagy receptor that provides cargo selectivity to autophagy. The four-tryptophan (FW) domain is a signature domain of Nbr1, but its exact function remains unclear. Here, we show that Nbr1 from the filamentous fungus Chaetomium thermophilum uses its FW domain to bind the α-mannosidase Ams1, a cargo of selective autophagy in both budding yeast and fission yeast, and delivers Ams1 to the vacuole by conventional autophagy in heterologous fission yeast. The structure of the Ams1-FW complex was determined at 2.2 Å resolution by cryo-electron microscopy. The FW domain adopts an immunoglobulin-like β-sandwich structure and recognizes the quaternary structure of the Ams1 tetramer. Notably, the N-terminal di-glycine of Ams1 is specifically recognized by a conserved pocket of the FW domain. The FW domain becomes degenerated in fission yeast Nbr1, which binds Ams1 with a ZZ domain instead. Our findings illustrate the protein binding mode of the FW domain and reveal the versatility of Nbr1-mediated cargo recognition.

Date: 2022
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DOI: 10.1038/s41467-022-31439-5

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