8HCU

Crystal structure of BCOR/PCGF1/KDM2B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Literature

Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation.

Chen, R.Shen, F.Zhang, Y.Sun, M.Dong, Y.Yin, Y.Su, C.Peng, C.Liu, J.Xu, J.

(2024) Commun Biol 7: 1112-1112

  • DOI: https://doi.org/10.1038/s42003-024-06820-3
  • Primary Citation of Related Structures:  
    8HCU

  • PubMed Abstract: 

    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 BCOR ANK-linker-PUFD /PCGF1 RAWUL . Through neutralizing negative charges of these Poly-D/E regions, Ca 2+ 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 Ca 2+ 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.


  • Organizational Affiliation

    Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B235Homo sapiensMutation(s): 0 
EC: 1.14.11.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHM5 (Homo sapiens)
Explore Q8NHM5 
Go to UniProtKB:  Q8NHM5
PHAROS:  Q8NHM5
GTEx:  ENSG00000089094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NHM5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb group RING finger protein 1105Homo sapiensMutation(s): 0 
Gene Names: PCGF1NSPC1RNF68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSM1 (Homo sapiens)
Explore Q9BSM1 
Go to UniProtKB:  Q9BSM1
PHAROS:  Q9BSM1
GTEx:  ENSG00000115289 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSM1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BCL-6 corepressor142Homo sapiensMutation(s): 0 
Gene Names: BCORKIAA1575
UniProt & NIH Common Fund Data Resources
Find proteins for Q6W2J9 (Homo sapiens)
Explore Q6W2J9 
Go to UniProtKB:  Q6W2J9
PHAROS:  Q6W2J9
GTEx:  ENSG00000183337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6W2J9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.291α = 90
b = 67.291β = 90
c = 252.035γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2017YFA0504104

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references, Structure summary