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(-) Description

Title :  SOLUTION NMR STRUCTURE OF THE CHROMO DOMAIN OF THE CHROMOBOX PROTEIN HOMOLOG 4
 
Authors :  L. Kaustov, A. Lemak, H. Quyang, C. Fares, A. Gutmanas, M. Ravichandran, P. Loppnau, C. Bountra, J. Weigelt, A. M. Edwards, J. Min, C. H. Arrowsmith, Structural Genomics Consortium (Sgc)
Date :  27 Mar 08  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Alpha/Beta Protein, Alternative Splicing, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation, Ubl Conjugation, Ubl Conjugation Pathway, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Kaustov, A. Lemak, H. Quyang, C. Fares, A. Gutmanas, M. Ravichandran, P. Loppnau, C. Bountra, J. Weigelt, A. M. Edwards, J. Min, C. H. Arrowsmith
Solution Nmr Structure Of The Chromo Domain Of The Chromobox Protein Homolog 4.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 SUMO-PROTEIN LIGASE CBX4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-MHL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCHROMO DOMAIN: RESIDUES 8-65
    GeneCBX4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHROMOBOX PROTEIN HOMOLOG 4, POLYCOMB 2 HOMOLOG, PC2, HPC2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2K28)

(-) Sites  (0, 0)

(no "Site" information available for 2K28)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K28)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX4_HUMAN11-69  1A:6-60
2CHROMO_1PS00598 Chromo domain signature.CBX4_HUMAN28-48  1A:23-43

(-) Exons   (0, 0)

(no "Exon" information available for 2K28)

(-) Sequences/Alignments

NMR Structure
   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:60
 aligned with CBX4_HUMAN | O00257 from UniProtKB/Swiss-Prot  Length:560

    Alignment length:60
                                    15        25        35        45        55        65
            CBX4_HUMAN    6 VGEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRERQEQ 65
               SCOP domains d2k28a_ A: automated matches                                 SCOP domains
               CATH domains 2k28A00 A:1-60  [code=2.40.50.40, no name defined]           CATH domains
               Pfam domains -----Chromo-2k28A01 A:6-55                             ----- Pfam domains
         Sec.struct. author .............eeee..eeeeee.....hhhhheeee.hhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----CHROMO_2  PDB: A:6-60 UniProt: 11-69                    PROSITE (1)
                PROSITE (2) ----------------------CHROMO_1  PDB: A:23-4----------------- PROSITE (2)
                 Transcript ------------------------------------------------------------ Transcript
                  2k28 A  1 GSEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRERQEQ 60
                                    10        20        30        40        50        60

   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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Tudor (88)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (CBX4_HUMAN | O00257)
molecular function
    GO:0032183    SUMO binding    Interacting selectively and non-covalently with the small ubiquitin-like protein SUMO.
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    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:0035102    PRC1 complex    A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling.
    GO:0031519    PcG protein complex    A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
    GO:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    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)

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        CBX4_HUMAN | O002573i8z 5epl

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