4R8P

Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle

Summary for 4R8P

• Entry DOI: 10.2210/pdb4r8p/pdb
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (9 entities in total)
• Functional Keywords: ring domain, arginine anchor, ubiquitin ligase, histone modification enzyme, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (clawed frog,common platanna,platanna); More
• Cellular location: Nucleus: P84233 P62799 P02281 P35226; Cell membrane ; Peripheral membrane protein : P61077
• Total number of polymer chains: 14
• Total formula weight: 284841.16

Authors

McGinty, R.K.,Henrici, R.C.,Tan, S. (deposition date: 2014-09-02, release date: 2014-11-05, Last modification date: 2023-09-20)

Primary citation

McGinty, R.K.,Henrici, R.C.,Tan, S.
Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome.
Nature, 514:591-596, 2014

PubMed Abstract: The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in many eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys 119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c. However, the molecular mechanism of nucleosome substrate recognition by PRC1 or other chromatin enzymes is unclear. Here we present the crystal structure of the human Ring1B-Bmi1-UbcH5c E3-E2 complex (the PRC1 ubiquitylation module) bound to its nucleosome core particle substrate. The structure shows how a chromatin enzyme achieves substrate specificity by interacting with several nucleosome surfaces spatially distinct from the site of catalysis. Our structure further reveals an unexpected role for the ubiquitin E2 enzyme in substrate recognition, and provides insight into how the related histone H2A E3 ligase, BRCA1, interacts with and ubiquitylates the nucleosome.

PubMed: 25355358
DOI: 10.1038/nature13890

Experimental method

X-RAY DIFFRACTION (3.2846 Å)