3O7A

Crystal structure of PHF13 in complex with H3K4me3

Summary for 3O7A

• Entry DOI: 10.2210/pdb3o7a/pdb
• Related: 3O70
• Descriptor: PHD finger protein 13 variant, H3K4ME3 HISTONE 11MER-PEPTIDE, GLYCEROL, ... (5 entities in total)
• Functional Keywords: phf13; zinc finger; phd domain, nuclear protein, structural genomics, structural genomics consortium, sgc, protein binding
• Biological source: Homo sapiens (human); More
• Cellular location: Chromosome . Nucleus : Q92133
• Total number of polymer chains: 2
• Total formula weight: 7574.60

Authors

Bian, C.B.,Lam, R.,Xu, C.,Bountra, C.,Arrowsmith, C.H.,Weigelt, J.,Edwards, A.M.,Bochkarev, A.,Min, J.,Structural Genomics Consortium (SGC) (deposition date: 2010-07-30, release date: 2010-10-06, Last modification date: 2023-09-06)

Primary citation

Chung, H.R.,Xu, C.,Fuchs, A.,Mund, A.,Lange, M.,Staege, H.,Schubert, T.,Bian, C.,Dunkel, I.,Eberharter, A.,Regnard, C.,Klinker, H.,Meierhofer, D.,Cozzuto, L.,Winterpacht, A.,Di Croce, L.,Min, J.,Will, H.,Kinkley, S.
PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3.
Elife, 5:-, 2016

PubMed Abstract: PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.

PubMed: 27223324
DOI: 10.7554/eLife.10607

Experimental method

X-RAY DIFFRACTION (1.67 Å)