9BAQ image
Entry Detail
PDB ID:
9BAQ
EMDB ID:
EMD-44411
Keywords:
Transferase/DNA Binding Protein/DNA
Title:
CryoEM structure of DIM2-HP1-H3K9me3-DNA complex
Biological Source:
Source Organism:
Neurospora crassa
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2024-04-04
Release Date:
2024-07-24
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.79 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9BAQ validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA (cytosine-5-)-methyltransferase
Chain IDs:A
Chain Length:1244
Number of Molecules:1
Biological Source:Neurospora crassa
UniProt ID:Q96W73 Pfam ID:PF00145
Protein Blast
Polymer Type:polypeptide(L)
Description:Heterochromatin protein one
Chain IDs:B, C
Chain Length:268
Number of Molecules:2
Biological Source:Neurospora crassa
UniProt ID:Q870N8 Pfam ID:PF00385, PF01393
Protein Blast
Polymer Type:polypeptide(L)
Description:Histone H3.2
Chain IDs:D, E (auth: F)
Chain Length:25
Number of Molecules:2
Biological Source:Neurospora crassa
UniProt ID:P07041
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')
Chain IDs:F (auth: G)
Chain Length:18
Number of Molecules:1
Biological Source:Neurospora crassa
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3')
Chain IDs:G (auth: H)
Chain Length:18
Number of Molecules:1
Biological Source:Neurospora crassa
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
M3L D LYS modified residue
Ligand Molecules
SAH
ZN
Primary Citation
Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation.
Nat Commun 15 6815 6815 (2024)
PMID: 39122718 DOI: 10.1038/s41467-024-51246-4

Abstact

Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora. The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.

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Primary Citation of related structures
9BAQ