9VBS

Crystal structure of the coiled-coil of ALLO-1a

Summary for 9VBS

• Entry DOI: 10.2210/pdb9vbs/pdb
• Descriptor: Isoform a of Allophagy receptor allo-1 (2 entities in total)
• Functional Keywords: autophagy adaptor, ubiquitin binding, atg8 binding, protein binding
• Biological source: Caenorhabditis elegans
• Total number of polymer chains: 3
• Total formula weight: 39409.64

Authors

Noda, N.N. (deposition date: 2025-06-04, release date: 2025-12-10, Last modification date: 2026-01-14)

Primary citation

Norizuki, T.,Kushida, Y.,Sekimoto, T.,Sasaki, T.,Yamano, K.,Matsuda, N.,Sasaki, R.,Noda, N.N.,Sato, K.,Sato, M.
ALLO-1a is a ubiquitin-binding adaptor for allophagy in Caenorhabditis elegans.
J.Cell.Sci., 138:-, 2025

PubMed Abstract: In the nematode Caenorhabditis elegans, sperm-derived mitochondria and membranous organelles (MOs) are selectively degraded by autophagy in embryos in a process termed allophagy. For this process, ALLO-1 functions as an autophagy adaptor. The allo-1 gene encodes two splice isoforms, ALLO-1a and ALLO-1b, which have different C-terminal sequences and are predominantly targeted to MOs and paternal mitochondria, respectively. However, the mechanism by which ALLO-1 targets the paternal organelles remains unknown. In this study, X-ray crystallography analysis reveals that the C-terminal region of ALLO-1a forms a parallel coiled-coil structure. In addition, AlphaFold2-Multimer predicts that this region directly interacts with ubiquitin. We showed that ALLO-1a interacts with K48- and K63-linked polyubiquitin in vitro and found that the D355 residue of ALLO-1a at the predicted interface with ubiquitin is important for its ubiquitin binding in vitro and also for its MO targeting and MO degradation in embryos. These results suggest that ubiquitin is a marker for the recognition of MOs by the autophagy machinery in C. elegans embryos.

PubMed: 41234204
DOI: 10.1242/jcs.264252

Experimental method

X-RAY DIFFRACTION (2.401 Å)