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 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.5 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.

(2018) Structure 26: 85-95.e3

  • DOI: https://doi.org/10.1016/j.str.2017.11.022
  • Primary Citation of Related Structures:  
    4NW3, 4O64, 4PZI, 4Z3C, 5VC9, 5W9Q, 5W9S, 6ASB, 6ASD

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 2B
A, B, C
118Homo sapiensMutation(s): 0 
Gene Names: KDM2BCXXC2FBL10FBXL10JHDM1BPCCX2
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
N [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
H [auth A]
I [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Z [auth C]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.322α = 90
b = 107.322β = 90
c = 34.13γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Data collection
  • Version 1.2: 2014-10-29
    Changes: Structure summary
  • Version 1.3: 2018-01-03
    Changes: Database references
  • Version 1.4: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-28
    Changes: Data collection