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 

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: 10.1016/j.str.2016.07.011

  • 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┬ávitro assembly assays to identify minimal c ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 2B
A
281Homo sapiensMutation(s): 0 
Gene Names: KDM2B (CXXC2, FBL10, FBXL10, JHDM1B, PCCX2)
EC: 1.14.11.27
Find proteins for Q8NHM5 (Homo sapiens)
Go to Gene View: KDM2B
Go to UniProtKB:  Q8NHM5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S-phase kinase-associated protein 1
B
162Homo sapiensMutation(s): 0 
Gene Names: SKP1 (EMC19, OCP2, SKP1A, TCEB1L)
Find proteins for P63208 (Homo sapiens)
Go to Gene View: SKP1
Go to UniProtKB:  P63208
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polycomb group RING finger protein 1
C
109Homo sapiensMutation(s): 0 
Gene Names: PCGF1 (NSPC1, RNF68)
Find proteins for Q9BSM1 (Homo sapiens)
Go to Gene View: PCGF1
Go to UniProtKB:  Q9BSM1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
BCL-6 corepressor-like protein 1
D
122Homo sapiensMutation(s): 0 
Gene Names: BCORL1
Find proteins for Q5H9F3 (Homo sapiens)
Go to Gene View: BCORL1
Go to UniProtKB:  Q5H9F3
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.049α = 90.00
b = 73.796β = 90.00
c = 123.014γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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