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(-) Description

Title :  STRUCTURAL BASIS OF SELECTIVE BINDING OF NON-METHYLATED CPG ISLANDS (DNA-ACGT) BY THE CXXC DOMAIN OF CFP1
 
Authors :  C. Xu, C. Bian, F. Mackenzie, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consortium (Sgc)
Date :  04 Feb 11  (Deposition) - 23 Feb 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics Consortium, Sgc, Dna Binding, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Xu, C. Bian, R. Lam, A. Dong, J. Min
The Structural Basis For Selective Binding Of Non-Methylate Cpg Islands By The Cfp1 Cxxc Domain.
Nat Commun V. 2 227 2011
PubMed-ID: 21407193  |  Reference-DOI: 10.1038/NCOMMS1237

(-) Compounds

Molecule 1 - CPG-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21-V2R-PRARE2
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CXXC-TYPE ZN FINGER, RESIDUES 161-222
    Gene: CFP1, CGBP, CXXC1, PCCX1, PHF18
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CXXC-TYPE ZINC FINGER PROTEIN 1, PHD FINGER AND CXXC DOMAIN- CONTAINING PROTEIN 1
 
Molecule 2 - 5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'
    Chains: B, C
    Engineered: YES
    Fragment: DNA (NONMETHYLATED CPG ISLAND)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2PO41Ligand/IonPHOSPHATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:169 , CYS A:172 , CYS A:175 , CYS A:208BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWARECYS A:181 , CYS A:184 , CYS A:187 , CYS A:203BINDING SITE FOR RESIDUE ZN A 301
3AC3SOFTWAREHIS A:183 , LYS A:217BINDING SITE FOR RESIDUE PEG A 1
4AC4SOFTWAREALA A:166 , ARG A:167 , MET A:168BINDING SITE FOR RESIDUE PEG A 2
5AC5SOFTWAREDG C:10 , DG C:11 , HOH C:21 , HOH C:26BINDING SITE FOR RESIDUE PO4 C 13

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QMI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QMI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QMI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QMI)

(-) Exons   (0, 0)

(no "Exon" information available for 3QMI)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:52
 aligned with CXXC1_HUMAN | Q9P0U4 from UniProtKB/Swiss-Prot  Length:656

    Alignment length:52
                                   175       185       195       205       215  
          CXXC1_HUMAN   166 ARMCGECEACRRTEDCGHCDFCRDMKKFGGPNKIRQKCRLRQCQLRARESYK 217
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains zf-CXXC-3qmiA01 A:166-208                  --------- Pfam domains
         Sec.struct. author ......hhhhhh......hhhhhhhhhhh........hhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 3qmi A 166 ARMCGECEACRRTEDCGHCDFCRDMKKFGGPNKIRQKCRLRQCQLRARESYK 217
                                   175       185       195       205       215  


Chain B from PDB  Type:DNA  Length:12
                                            
                 3qmi B   1 GCCAACGTTGGC  12
                                    10  


Chain C from PDB  Type:DNA  Length:12
                                            
                 3qmi C   1 GCCAACGTTGGC  12
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3QMI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QMI)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: zf-CXXC] (8)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CXXC1_HUMAN | Q9P0U4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0045322    unmethylated CpG binding    Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0048188    Set1C/COMPASS complex    A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CXXC1_HUMAN | Q9P0U4: 3qmb 3qmc 3qmd 3qmg 3qmh

(-) Related Entries Specified in the PDB File

3qmb THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA.
3qmc THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA.
3qmd THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA.
3qmg THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA.
3qmh THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA.