SNAP output for PDB entry 7lyb [SNAP web server]

PDB-id

7lyb; SNAP-derived features in text and JSON formats; DNAproDB

Class

structural protein-DNA

Method

cryo-EM (3.28 Å)

Summary

cryo-EM structure of the human nucleosome core particle in complex with brca1-bard1-ubch5c

Reference

Hu Q, Botuyan MV, Zhao D, Cui G, Mer E, Mer G (2021): "Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation." Nature, 596, 438-443. doi: 10.1038/s41586-021-03716-8.

Abstract

The BRCA1-BARD1 tumour suppressor is an E3 ubiquitin ligase necessary for the repair of DNA double-strand breaks by homologous recombination_1-10. The BRCA1-BARD1 complex localizes to damaged chromatin after DNA replication and catalyses the ubiquitylation of histone H2A and other cellular targets_11-14. The molecular bases for the recruitment to double-strand breaks and target recognition of BRCA1-BARD1 remain unknown. Here we use cryo-electron microscopy to show that the ankyrin repeat and tandem BRCT domains in BARD1 adopt a compact fold and bind to nucleosomal histones, DNA and monoubiquitin attached to H2A amino-terminal K13 or K15, two signals known to be specific for double-strand breaks_15,16. We further show that RING domains₁₇ in BRCA1-BARD1 orient an E2 ubiquitin-conjugating enzyme atop the nucleosome in a dynamic conformation, primed for ubiquitin transfer to the flexible carboxy-terminal tails of H2A and variant H2AX. Our work reveals a regulatory crosstalk in which recognition of monoubiquitin by BRCA1-BARD1 at the N terminus of H2A blocks the formation of polyubiquitin chains and cooperatively promotes ubiquitylation at the C terminus of H2A. These findings elucidate the mechanisms of BRCA1-BARD1 chromatin recruitment and ubiquitylation specificity, highlight key functions of BARD1 in both processes and explain how BRCA1-BARD1 promotes homologous recombination by opposing the DNA repair protein 53BP1 in post-replicative chromatin_18-22. These data provide a structural framework to evaluate BARD1 variants and help to identify mutations that drive the development of cancer.