3QMD

Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1038/ncomms1237
  • Primary Citation of Related Structures:  
    3QMB, 3QMC, 3QMD, 3QMG, 3QMH, 3QMI

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CpG-binding protein79Homo sapiensMutation(s): 0 
Gene Names: CXXC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U4 (Homo sapiens)
Explore Q9P0U4 
Go to UniProtKB:  Q9P0U4
GTEx:  ENSG00000154832 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0U4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*AP*TP*GP*GP*C)-3')12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*CP*AP*TP*CP*GP*TP*TP*GP*GP*C)-3')12N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.653α = 90
b = 74.688β = 90
c = 125.769γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
EPICS-baseddata collection
datadata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description