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(-) Description

Title :  SOLUTION STRUCTURE OF THE ARID DOMAIN OF JARID1D PROTEIN
 
Authors :  W. Tanabe, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Arid Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Tanabe, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Arid Domain Of Jarid1D Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1D
    ChainsA
    EngineeredYES
    Expression System PlasmidP060731-15
    Expression System Vector TypePLASMID
    FragmentARID DOMAIN
    GeneSMCY, HY, HYA, JARID1D, KIAA0234
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN SMCY, HISTOCOMPATIBILITY Y ANTIGEN, H-Y

 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 2YQE)

(-) Sites  (0, 0)

(no "Site" information available for 2YQE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARIDPS51011 ARID domain profile.KDM5D_HUMAN79-169  1A:79-169

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003179611aENSE00001733393Y:21906809-21906557253KDM5D_HUMAN-00--
1.2ENST000003179612ENSE00000891759Y:21906439-21906271169KDM5D_HUMAN1-50501A:72-754
1.3ENST000003179613ENSE00000652508Y:21905125-2190504878KDM5D_HUMAN51-76261A:76-761
1.4ENST000003179614ENSE00000652506Y:21903743-21903621123KDM5D_HUMAN77-117411A:77-11741
1.5ENST000003179615ENSE00001788914Y:21903374-21903204171KDM5D_HUMAN118-174571A:118-17154
1.6ENST000003179616ENSE00001805865Y:21901548-21901414135KDM5D_HUMAN175-219450--
1.7ENST000003179617ENSE00000652503Y:21897636-21897507130KDM5D_HUMAN220-263440--
1.8ENST000003179618ENSE00000652502Y:21897383-21897238146KDM5D_HUMAN263-311490--
1.9ENST000003179619ENSE00000652501Y:21894628-21894470159KDM5D_HUMAN312-364530--
1.10ENST0000031796110ENSE00001799734Y:21894051-21893932120KDM5D_HUMAN365-404400--
1.11ENST0000031796111ENSE00000652498Y:21893816-21893658159KDM5D_HUMAN405-457530--
1.12cENST0000031796112cENSE00001786866Y:21883197-21883016182KDM5D_HUMAN458-518610--
1.13ENST0000031796113ENSE00001788639Y:21882920-21882758163KDM5D_HUMAN518-572550--
1.14aENST0000031796114aENSE00001628770Y:21878601-21878482120KDM5D_HUMAN573-612400--
1.15aENST0000031796115aENSE00000652494Y:21878359-21878165195KDM5D_HUMAN613-677650--
1.16bENST0000031796116bENSE00001706456Y:21877890-21877709182KDM5D_HUMAN678-738610--
1.17aENST0000031796117aENSE00001758341Y:21877625-21877501125KDM5D_HUMAN738-780430--
1.17cENST0000031796117cENSE00000652491Y:21877385-21877238148KDM5D_HUMAN780-829500--
1.18bENST0000031796118bENSE00000652489Y:21872358-2187226297KDM5D_HUMAN829-861330--
1.18eENST0000031796118eENSE00001277224Y:21871695-21871337359KDM5D_HUMAN862-9811200--
1.19aENST0000031796119aENSE00001741532Y:21870899-21870761139KDM5D_HUMAN981-1027470--
1.20bENST0000031796120bENSE00001674577Y:21870309-21870130180KDM5D_HUMAN1028-1087600--
1.21ENST0000031796121ENSE00001630270Y:21869957-21869820138KDM5D_HUMAN1088-1133460--
1.22bENST0000031796122bENSE00000652484Y:21869632-21869033600KDM5D_HUMAN1134-13332000--
1.23aENST0000031796123aENSE00001670444Y:21868749-2186868070KDM5D_HUMAN1334-1357240--
1.23cENST0000031796123cENSE00001594027Y:21868526-21868327200KDM5D_HUMAN1357-1423670--
1.24dENST0000031796124dENSE00001945799Y:21868231-21867301931KDM5D_HUMAN1424-15391160--

(-) 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:100
 aligned with KDM5D_HUMAN | Q9BY66 from UniProtKB/Swiss-Prot  Length:1539

    Alignment length:133
                                    48        58        68        78        88        98       108       118       128       138       148       158       168   
          KDM5D_HUMAN    39 EKSGICKIRPPADWQPPFAVEVDNFRFTPRVQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQSGA 171
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------ARID-2yqeA01 A:79-165                                                                  ------ Pfam domains
         Sec.struct. author ....---------------------------------....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------ARID  PDB: A:79-169 UniProt: 79-169                                                        -- PROSITE
               Transcript 1 Exon 1.2    Exon 1.3  PDB: A:76-76    Exon 1.4  PDB: A:77-117 UniProt: 77-117  Exon 1.5  PDB: A:118-171 UniProt: 118-174 [INCOMPLETE] Transcript 1
                 2yqe A  72 GSSG---------------------------------SSGTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQSGA 171
                               |     -         -         -       |78        88        98       108       118       128       138       148       158       168   
                              75                                76                                                                                               

   Legend:   → Mismatch (orange background)
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  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 2YQE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (KDM5D_HUMAN | Q9BY66)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0032453    histone demethylase activity (H3-K4 specific)    Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0002457    T cell antigen processing and presentation    The process in which a T cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0034720    histone H3-K4 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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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        KDM5D_HUMAN | Q9BY662e6r

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