3QMG | pdb_00003qmg

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

• PDB DOI: https://doi.org/10.2210/pdb3QMG/pdb
• NAKB: 3QMG

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-02-04 Released: 2011-02-23 
• Deposition Author(s): Xu, C., Bian, C., MacKenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.279 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

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

• PubMed: 21407193 
• DOI: https://doi.org/10.1038/ncomms1237
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.09 kDa 
• Atom Count: 911 
• Modeled Residue Count: 76 
• Deposited Residue Count: 103 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CpG-binding protein	A	79	Homo sapiens	Mutation(s): 0  Gene Names: CFP1, CGBP, CXXC1, PCCX1, PHF18
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U4 (Homo sapiens) Explore Q9P0U4  Go to UniProtKB:  Q9P0U4
PHAROS:  Q9P0U4 GTEx:  ENSG00000154832

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*CP*AP*AP*CP*GP*GP*TP*GP*GP*C)-3'	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*CP*AP*CP*CP*GP*TP*TP*GP*GP*C)-3'	C	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.279 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.436	α = 90
b = 74.91	β = 90
c = 125.755	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Xu, C., Bian, C., MacKenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

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