Cross-linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex

The multi-subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or recombinantly reconstitute the complex for structural studies have proven quite challenging. Until now, only substructures of individual domains or proteins and low-resolution densities of (partial) complexes have been reported. In this study, we comprehensively investigated the relative orientation of different subunits within the NuRD complex using multiple cross-link IP mass spectrometry (xIP-MS) experiments. Our results confirm that the core of the complex is formed by MTA, RBBP, and HDAC proteins. Assembly of a copy of MBD and GATAD2 onto this core enables binding of the peripheral CHD and CDK2AP proteins. Furthermore, our experiments reveal that not only CDK2AP1 but also CDK2AP2 interacts with the NuRD complex. This interaction requires the C terminus of CHD proteins. Our data provide a more detailed understanding of the topology of the peripheral NuRD subunits relative to the core complex. Database Proteomics data are available in the PRIDE database under the accession numbers PXD017244 and PXD017378.

Automated summary

The study investigates the relative orientation of different subunits within the NuRD complex using multiple cross-link IP mass spectrometry experiments, confirming that the core of the complex consists of MTA, RBBP, and HDAC proteins. It also reveals interactions between CDK2AP1 and CDK2AP2 with the NuRD complex, shedding light on the topology of peripheral NuRD subunits relative to the core complex. The data provide a more detailed understanding of the assembly and structure of the NuRD complex.