3QMG

Structural Basis of Selective Binding of Non-Methylated CpG islands by the CXXC Domain of CFP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.

Xu, C.Bian, C.Lam, R.Dong, A.Min, J.

(2011) Nat Commun 2: 227-227

  • DOI: 10.1038/ncomms1237
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CFP1 is a CXXC domain-containing protein and an essential component of the SETD1 histone H3K4 methyltransferase complex. CXXC domain proteins direct different chromatin-modifying activities to various chromatin regions. Here, we report crystal struct ...

    CFP1 is a CXXC domain-containing protein and an essential component of the SETD1 histone H3K4 methyltransferase complex. CXXC domain proteins direct different chromatin-modifying activities to various chromatin regions. Here, we report crystal structures of the CFP1 CXXC domain in complex with six different CpG DNA sequences. The crescent-shaped CFP1 CXXC domain is wedged into the major groove of the CpG DNA, distorting the B-form DNA, and interacts extensively with the major groove of the DNA. The structures elucidate the molecular mechanism of the non-methylated CpG-binding specificity of the CFP1 CXXC domain. The CpG motif is confined by a tripeptide located in a rigid loop, which only allows the accommodation of the non-methylated CpG dinucleotide. Furthermore, we demonstrate that CFP1 has a preference for a guanosine nucleotide following the CpG motif.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CpG-binding protein
A
79Homo sapiensMutation(s): 0 
Gene Names: CXXC1 (CFP1, CGBP, PCCX1, PHF18)
Find proteins for Q9P0U4 (Homo sapiens)
Go to Gene View: CXXC1
Go to UniProtKB:  Q9P0U4
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*CP*AP*AP*CP*GP*GP*TP*GP*GP*C)-3'B12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*CP*CP*AP*CP*CP*GP*TP*TP*GP*GP*C)-3'C12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 30.436α = 90.00
b = 74.910β = 90.00
c = 125.755γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance