8HCU image
Deposition Date 2022-11-03
Release Date 2023-11-15
Last Version Date 2024-10-30
Entry Detail
PDB ID:
8HCU
Keywords:
Title:
Crystal structure of BCOR/PCGF1/KDM2B complex
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 43 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B
Chain IDs:A
Chain Length:235
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polycomb group RING finger protein 1
Gene (Uniprot):PCGF1
Chain IDs:B
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:BCL-6 corepressor
Gene (Uniprot):BCOR
Chain IDs:C
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation.
Commun Biol 7 1112 1112 (2024)
PMID: 39256555 DOI: 10.1038/s42003-024-06820-3

Abstact

Recruitment of non-canonical BCOR-PRC1.1 to non-methylated CpG islands via KDM2B plays a fundamental role in transcription control during developmental processes and cancer progression. However, the mechanism is still largely unknown on how this recruitment is regulated. Here, we unveiled the importance of the Poly-D/E regions within the linker of BCOR for its binding to KDM2B. Interestingly, we also demonstrated that these negatively charged Poly-D/E regions on BCOR play autoinhibitory roles in liquid-liquid phase separation (LLPS) of BCORANK-linker-PUFD/PCGF1RAWUL. Through neutralizing negative charges of these Poly-D/E regions, Ca2+ not only weakens the interaction between BCOR/PCGF1 and KDM2B, but also promotes co-condensation of the enzymatic core of BCOR-PRC1.1 with KDM2B into liquid-like droplet. Accordingly, we propose that Ca2+ could modulate the compartmentation and recruitment of the enzymatic core of BCOR-PRC1.1 on KDM2B target loci. Thus, our finding advances the mechanistic understanding on how the tethering of BCOR-PRC1.1 enzymatic core to KDM2B is regulated.

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Primary Citation of related structures