6BHE image
Entry Detail
PDB ID:
6BHE
Keywords:
Title:
Crystal structure of SETDB1 with a modified H3 peptide
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2017-10-30
Release Date:
2017-12-06
Method Details:
Experimental Method:
Resolution:
1.35 Å
R-Value Free:
0.17
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Histone-lysine N-methyltransferase SETDB1
Chain IDs:A
Chain Length:239
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H3.1
Chain IDs:B
Chain Length:18
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ALY B LYS modified residue
M3L B LYS modified residue
Ligand Molecules
Primary Citation
H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1.
Nat Commun 8 2057 2057 (2017)
PMID: 29234025 DOI: 10.1038/s41467-017-02259-9

Abstact

SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.

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Primary Citation of related structures