4O64

Zinc fingers of KDM2B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.

Xu, C.Liu, K.Lei, M.Yang, A.Li, Y.Hughes, T.R.Min, J.

(2017) Structure --: --

  • DOI: 10.1016/j.str.2017.11.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The CXXC domain, first identified as the reader of unmodified CpG dinucleotide, plays important roles in epigenetic regulation by targeting various activities to CpG islands. Here we systematically measured and compared the DNA-binding selectivities ...

    The CXXC domain, first identified as the reader of unmodified CpG dinucleotide, plays important roles in epigenetic regulation by targeting various activities to CpG islands. Here we systematically measured and compared the DNA-binding selectivities of all known human CXXC domains by different binding assays, and complemented the existing function-based classification of human CXXC domains with a classification based on their DNA selectivities. Through a series of crystal structures of CXXC domains with DNA ligands, we unravel the molecular mechanisms of how these CXXC domains, including single CXXC domains and tandem CXXC-PHD domains, recognize distinct DNA ligands, which further supports our classification of human CXXC domains and also provides insights into selective recruitment of chromatin modifiers to their respective targets via CXXC domains recognizing different genomic DNA sequences. Our study facilitates the understanding of the relationship between the DNA-binding specificities of the CXXC proteins and their biological functions.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 2B
A, B, C
118Homo 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 107.322α = 90.00
b = 107.322β = 90.00
c = 34.130γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
Aimlessdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Data collection
  • Version 1.2: 2014-10-29
    Type: Structure summary
  • Version 1.3: 2018-01-03
    Type: Database references