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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SPOC DOMAIN OF THE HUMAN TRANSCRIPTIONAL COREPRESSOR, SHARP.
 
Authors :  J. W. Schwabe, M. Ariyoshi
Date :  28 Mar 03  (Deposition) - 19 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Barrel, Spoc Domain, , Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Schwabe, M. Ariyoshi
A Conserved Structural Motif Reveals The Essential Transcriptional Repression Function Of Spen Proteins And Their Role In Developmental Signaling
Genes Dev. V. 17 1909 2003
PubMed-ID: 12897056  |  Reference-DOI: 10.1101/GAD.266203
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMART/HDAC1 ASSOCIATED REPRESSOR PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainROSSETTA BL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSPOC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMSX2 INTERACTING NUCLEAR TARGET (MINT) HOMOLOG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1OW1)

(-) Sites  (0, 0)

(no "Site" information available for 1OW1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OW1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OW1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OW1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SPOCPS50917 SPOC domain profile.MINT_HUMAN3498-3664  1A:3498-3664

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003757591ENSE00001468313chr1:16174359-16174645287MINT_HUMAN1-28280--
1.2ENST000003757592ENSE00001065383chr1:16199311-16199631321MINT_HUMAN28-1351080--
1.4aENST000003757594aENSE00000955468chr1:16202697-16203173477MINT_HUMAN135-2941600--
1.5aENST000003757595aENSE00000827972chr1:16235816-16235976161MINT_HUMAN294-348550--
1.6ENST000003757596ENSE00002153898chr1:16237596-16237796201MINT_HUMAN348-415680--
1.7ENST000003757597ENSE00001734774chr1:16242623-16242774152MINT_HUMAN415-465510--
1.8ENST000003757598ENSE00001633894chr1:16245421-16245546126MINT_HUMAN466-507420--
1.9ENST000003757599ENSE00001776313chr1:16245899-16246012114MINT_HUMAN508-545380--
1.10bENST0000037575910bENSE00001771430chr1:16247365-16247478114MINT_HUMAN546-583380--
1.11ENST0000037575911ENSE00001597480chr1:16248744-16248844101MINT_HUMAN584-617340--
1.12bENST0000037575912bENSE00000827978chr1:16254586-162627618176MINT_HUMAN617-334227260--
1.13ENST0000037575913ENSE00000751295chr1:16263658-16264140483MINT_HUMAN3343-35031611A:3495-35039
1.14ENST0000037575914ENSE00000827979chr1:16264307-16264501195MINT_HUMAN3504-3568651A:3504-3568 (gaps)65
1.15bENST0000037575915bENSE00000827980chr1:16265213-16265371159MINT_HUMAN3569-3621531A:3569-362153
1.16bENST0000037575916bENSE00001468270chr1:16265791-162669551165MINT_HUMAN3622-3664431A:3622-366443

(-) 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:167
 aligned with MINT_HUMAN | Q96T58 from UniProtKB/Swiss-Prot  Length:3664

    Alignment length:170
                                  3504      3514      3524      3534      3544      3554      3564      3574      3584      3594      3604      3614      3624      3634      3644      3654      3664
          MINT_HUMAN   3495 PVDMVQLLKKYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGGPPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIASV 3664
               SCOP domains d1ow1a_ A: SMART/HDAC1 associated repressor pro   tein, SHARP                                                                                                              SCOP domains
               CATH domains 1ow1A00 A:3495-3664  [code=2.40.290.10, no name    defined]                                                                                                                CATH domains
               Pfam domains --------------SPOC-1ow1A01 A:3509-3630                                                                                                  ---------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.eeeeeeeee..eeeeeeeeeeeehhhhhhhhh...---..eee.eeee.hhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhheeeeeee.........eeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SPOC  PDB: A:3498-3664 UniProt: 3498-3664                                                                                                                               PROSITE
               Transcript 1 Exon 1.13Exon 1.14  PDB: A:3504-3568 (gaps) UniProt: 3504-3568            Exon 1.15b  PDB: A:3569-3621 UniProt: 3569-3621      Exon 1.16b  PDB: A:3622-3664                Transcript 1
                1ow1 A 3495 PVDMVQLLKKYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLS---PPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIASV 3664
                                  3504      3514      3524      3534      |  -|     3554      3564      3574      3584      3594      3604      3614      3624      3634      3644      3654      3664
                                                                       3541   |                                                                                                                       
                                                                           3545                                                                                                                       

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MINT_HUMAN | Q96T58)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0001191    transcriptional repressor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    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:0050769    positive regulation of neurogenesis    Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MINT_HUMAN | Q96T582rt5 4p6q

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