4H75

Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide

Summary for 4H75

• Entry DOI: 10.2210/pdb4h75/pdb
• Descriptor: Spindlin-1, Histone H3, GLYCEROL, ... (6 entities in total)
• Functional Keywords: tudor domain, h3k4me3 binding, methylation, gene regulation
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q9Y657
• Total number of polymer chains: 2
• Total formula weight: 28692.46

Authors

Yang, N.,Wang, W.,Wang, Y.,Wang, M.,Zhao, Q.,Rao, Z.,Zhu, B.,Xu, R.M. (deposition date: 2012-09-20, release date: 2012-10-03, Last modification date: 2023-09-20)

Primary citation

Yang, N.,Wang, W.,Wang, Y.,Wang, M.,Zhao, Q.,Rao, Z.,Zhu, B.,Xu, R.M.
Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1.
Proc.Natl.Acad.Sci.USA, 109:17954-17959, 2012

PubMed Abstract: Recognition of methylated histone tail lysine residues by tudor domains plays important roles in epigenetic control of gene expression and DNA damage response. Previous studies revealed the binding of methyllysine in a cage of aromatic residues, but the molecular mechanism by which the sequence specificity for surrounding histone tail residues is achieved remains poorly understood. In the crystal structure of a trimethylated histone H3 lysine 4 (H3K4) peptide bound to the tudor-like domains of Spindlin1 presented here, an atypical mode of methyllysine recognition by an aromatic pocket of Spindlin1 is observed. Furthermore, the histone sequence is recognized in a distinct manner involving the amino terminus and a pair of arginine residues of histone H3, and disruption of the binding impaired stimulation of pre-RNA expression by Spindlin1. Our analysis demonstrates considerable diversities of methyllysine recognition and sequence-specific binding of histone tails by tudor domains, and the revelation furthers the understanding of tudor domain proteins in deciphering epigenetic marks on histone tails.

PubMed: 23077255
DOI: 10.1073/pnas.1208517109

Experimental method

X-RAY DIFFRACTION (2.098 Å)