5JH5

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1.

Wong, S.J.Gearhart, M.D.Taylor, A.B.Nanyes, D.R.Ha, D.J.Robinson, A.K.Artigas, J.A.Lee, O.J.Demeler, B.Hart, P.J.Bardwell, V.J.Kim, C.A.

(2016) Structure 24: 1795-1801

  • DOI: https://doi.org/10.1016/j.str.2016.07.011
  • Primary Citation of Related Structures:  
    5JH5

  • PubMed Abstract: 

    KDM2B recruits H2A-ubiquitinating activity of a non-canonical Polycomb Repression Complex 1 (PRC1.1) to CpG islands, facilitating gene repression. We investigated the molecular basis of recruitment using in vitro assembly assays to identify minimal components, subcomplexes, and domains required for recruitment. A minimal four-component PRC1.1 complex can be assembled by combining two separately isolated subcomplexes: the DNA-binding KDM2B/SKP1 heterodimer and the heterodimer of BCORL1 and PCGF1, a core component of PRC1.1. The crystal structure of the KDM2B/SKP1/BCORL1/PCGF1 complex illustrates the crucial role played by the PCGF1/BCORL1 heterodimer. The BCORL1 PUFD domain positions residues preceding the RAWUL domain of PCGF1 to create an extended interface for interaction with KDM2B, which is unique to the PCGF1-containing PRC1.1 complex. The structure also suggests how KDM2B might simultaneously function in PRC1.1 and an SCF ubiquitin ligase complex and the possible molecular consequences of BCOR PUFD internal tandem duplications found in pediatric kidney and brain tumors.


  • Organizational Affiliation

    Department of Biochemistry and CTRC, University of Texas Health Science Center at San Antonio, MSC 7760, 7703 Floyd Curl Drive, San Antonio, TX 78229-3990, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 2B281Homo sapiensMutation(s): 0 
Gene Names: KDM2BCXXC2FBL10FBXL10JHDM1BPCCX2
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
S-phase kinase-associated protein 1162Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558 
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UniProt GroupP63208
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb group RING finger protein 1109Homo 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 
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UniProt GroupQ9BSM1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
BCL-6 corepressor-like protein 1122Homo sapiensMutation(s): 0 
Gene Names: BCORL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5H9F3 (Homo sapiens)
Explore Q5H9F3 
Go to UniProtKB:  Q5H9F3
PHAROS:  Q5H9F3
GTEx:  ENSG00000085185 
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UniProt GroupQ5H9F3
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.049α = 90
b = 73.796β = 90
c = 123.014γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references