8TLF image
Entry Detail
PDB ID:
8TLF
Title:
CDCA7 (Mouse) Binds Non-B-form DNA oligo 36-mer (sg C2-Form 2)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-07-26
Release Date:
2024-08-21
Method Details:
Experimental Method:
Resolution:
1.64 Å
R-Value Free:
0.21
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Cell division cycle-associated protein 7
Chain IDs:A, B
Chain Length:144
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polydeoxyribonucleotide
Description:ssDNA
Chain IDs:C (auth: X), D (auth: Y)
Chain Length:36
Number of Molecules:2
Biological Source:Mus musculus
Primary Citation
The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA.
Biorxiv ? ? ? (2023)
PMID: 38168392 DOI: 10.1101/2023.12.15.571946

Abstact

CDCA7 , encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.

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Primary Citation of related structures