The mitosis and neurodevelopment proteins NDE1 and NDEL1 form dimers, tetramers and polymers with a folded-back structure in solution

Paralogs NDE1 (Nuclear Distribution Element 1) and NDEL1 (NDE-Like 1) are essential for mitosis and neurodevelopment. Both proteins are predicted to have similar structures, based upon high sequence similarity and they co-complex in mammalian cells. X-ray diffraction studies and homology modeling suggests their N-terminal regions (residues 8-167) adopt continuous, extended alpha-helical coiled-coil structures, but no experimentally derived information on the structure of their C-terminal regions or the architecture of the full-length proteins is available. In the case of NDE1, no biophysical data exists. Here we characterize the structural architecture of both full-length proteins utilizing negative-stain electron microscopy along with our established paradigm of chemical cross-linking followed by tryptic digestion, mass spectrometry and database searching, which we enhance using isotope-labeling for mixed NDE1-NDEL1. We determined that full-length NDE1 forms needle-like dimers and tetramers in solution, similar to crystal structures of NDEL1, as well as chain-like end-to-end polymers. The C-terminal domain of each protein, required for interaction with key protein partners dynein and Disrupted-In-Schizophrenia 1 (DISC1), includes a predicted disordered region that allows a bent-back structure. This facilitates interaction of the C-terminal region with the N-terminal coiled-coil domain, and is in agreement with previous results showing N- and C-terminal regions of NDEL1 and NDE1 cooperating in dynein interaction. It sheds light on recently identified mutations in the NDE1 gene that cause truncation of the encoded protein. Additionally, analysis of mixed NDE1-NDEL1 complexes demonstrates that NDE1 and NDEL1 can interact directly.