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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-064, A CHROMO DOMAIN FROM HUMAN CDNA
 
Authors :  A. Z. M. Ruhul Momen, H. Hirota, K. Izumi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 06  (Deposition) - 26 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Chromo Domain, Histone H3 Tail, Choromatin Organization Modifier, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Z. M. Ruhul Momen, H. Hirota, K. Izumi, M. Yoshida, S. Yokoyama
Solution Structure Of Rsgi Ruh-064, A Chromo Domain From Human Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE, ISOFORM B
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050829-10
    Expression System Vector TypePLASMID
    FragmentMETHYLATED HISTONE H3 TAIL BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 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 2DNT)

(-) Sites  (0, 0)

(no "Site" information available for 2DNT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032939A60GCDYL1_HUMANPolymorphism28360500AL13G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CDYL1_HUMAN61-121  1A:16-73
2CHROMO_1PS00598 Chromo domain signature.CDYL1_HUMAN79-99  1A:32-52

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003289081bENSE00001241571chr6:4706393-470648593CDYL1_HUMAN-00--
1.2aENST000003289082aENSE00002154059chr6:4715975-4716115141CDYL1_HUMAN1-35350--
1.4ENST000003289084ENSE00001979662chr6:4734996-473507883CDYL1_HUMAN35-62281A:1-15 (gaps)23
1.9dENST000003289089dENSE00001979701chr6:4891947-4892613667CDYL1_HUMAN63-2852231A:16-78 (gaps)71
1.11bENST0000032890811bENSE00001972080chr6:4935749-4936005257CDYL1_HUMAN285-370860--
1.12ENST0000032890812ENSE00001991020chr6:4937799-4937971173CDYL1_HUMAN371-428580--
1.13bENST0000032890813bENSE00001960715chr6:4943780-4943990211CDYL1_HUMAN428-498710--
1.14ENST0000032890814ENSE00001962725chr6:4952500-4952643144CDYL1_HUMAN499-546480--
1.15eENST0000032890815eENSE00001930193chr6:4954132-49557811650CDYL1_HUMAN547-598520--

(-) 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:78
 aligned with CDYL1_HUMAN | Q9Y232 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:94
                                    49        59        69        79        89        99       109       119       129    
          CDYL1_HUMAN    40 GPSDPSISVSSEQSGAQQPPALQVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNRRHTEKQKESTLTRTNRTSPNNA 133
               SCOP domains ---------------d2dnta1 A:8-73 Chromodomain protein, Y-like isoform               ------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------.................eeeeee.....eeeee.....hhhhheeee......hhhhhhhhhhhhh......--------..... Sec.struct. author
                 SAPs(SNPs) --------------------G------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------CHROMO_2  PDB: A:16-73 UniProt: 61-121                       ------------ PROSITE (1)
                PROSITE (2) ---------------------------------------CHROMO_1  PDB: A:32-5---------------------------------- PROSITE (2)
               Transcript 1 Exon 1.4 UniProt: 35-62Exon 1.9d  PDB: A:16-78 (gaps) UniProt: 63-285 [INCOMPLETE]             Transcript 1
                 2dnt A   1 G--------SSGSSGMASEELYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNRRHTEKQKES--------GPSSG  78
                            |        2        12        22        32        42        52        62        72|       74    
                            |        2                                                                     73       74    
                            1                                                                                             

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    → 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  (0, 0)

(no "CATH Domain" information available for 2DNT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DNT)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (CDYL1_HUMAN | Q9Y232)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    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: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: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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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

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UniProtKB/Swiss-Prot
        CDYL1_HUMAN | Q9Y2322gtr

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