5W9Q

Zinc finger region of MBD1 in complex with CpG DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.str.2017.11.022
  • Primary Citation of Related Structures:  4NW3, 4O64, 4PZI, 4Z3C, 5VC9, 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 ...

    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
Methyl-CpG-binding domain protein 1
A, B
60Homo sapiensGene Names: MBD1 (CXXC3, PCM1)
Find proteins for Q9UIS9 (Homo sapiens)
Go to Gene View: MBD1
Go to UniProtKB:  Q9UIS9
Entity ID: 2
MoleculeChainsLengthOrganism
dnaC,D,E,F12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 139.339α = 90.00
b = 27.800β = 106.52
c = 64.914γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references
  • Version 1.2: 2018-01-10
    Type: Database references