8DU4

Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome

Summary for 8DU4

• Entry DOI: 10.2210/pdb8du4/pdb
• Related: 7UD5
• EMDB information: 26454 27715
• Descriptor: Histone H3, Histone H4, Histone H2A, ... (9 entities in total)
• Functional Keywords: ubiquitin, chromatin, mll, methylation, dna binding protein
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 13
• Total formula weight: 304201.38

Authors

Niklas, H.A.,Rahman, S.,Worden, E.J.,Wolberger, C. (deposition date: 2022-07-26, release date: 2022-09-21, Last modification date: 2024-10-23)

Primary citation

Rahman, S.,Hoffmann, N.A.,Worden, E.J.,Smith, M.L.,Namitz, K.E.W.,Knutson, B.A.,Cosgrove, M.S.,Wolberger, C.
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome.
Proc.Natl.Acad.Sci.USA, 119:e2205691119-e2205691119, 2022

PubMed Abstract: The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, DR5, bBp5, sh2L, and PY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.

PubMed: 36095189
DOI: 10.1073/pnas.2205691119

Experimental method

ELECTRON MICROSCOPY (3.55 Å)