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(-) Description

Title :  SOLUTION STRUCTURE OF THE BROMODOMAIN OF HUMAN BRD7 PROTEIN
 
Authors :  H. Sun, J. Liu, J. Zhang, H. Huang, J. Wu, Y. Shi
Date :  31 Aug 06  (Deposition) - 10 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Helix, Left-Handed Four-Helix Bundle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Sun, J. Liu, J. Zhang, W. Shen, H. Huang, C. Xu, H. Dai, J. Wu, Y. Shi
Solution Structure Of Brd7 Bromodomain And Its Interaction With Acetylated Peptides From Histone H3 And H4
Biochem. Biophys. Res. Commun. V. 358 435 2007
PubMed-ID: 17498659  |  Reference-DOI: 10.1016/J.BBRC.2007.04.139
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 7
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentBROMODOMAIN
    GeneBRD7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBRAIN
    Synonym75 KDA BROMODOMAIN PROTEIN, PROTEIN CELTIX-1

 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 2I7K)

(-) Sites  (0, 0)

(no "Site" information available for 2I7K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I7K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I7K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I7K)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.BRD7_HUMAN148-218  1A:20-90

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003946881aENSE00001519214chr16:50402845-50402637209BRD7_HUMAN1-17170--
1.2ENST000003946882ENSE00001141771chr16:50402209-50402001209BRD7_HUMAN17-86700--
1.4ENST000003946884ENSE00001141766chr16:50388833-50388704130BRD7_HUMAN87-130441A:0-23
1.5ENST000003946885ENSE00001141759chr16:50388393-5038833658BRD7_HUMAN130-149201A:2-2120
1.6ENST000003946886ENSE00001141755chr16:50384078-50383934145BRD7_HUMAN149-197491A:21-6949
1.8ENST000003946888ENSE00001141753chr16:50373997-50373887111BRD7_HUMAN198-234371A:70-10637
1.9ENST000003946889ENSE00001141751chr16:50368806-50368622185BRD7_HUMAN235-296621A:107-11610
1.10ENST0000039468810ENSE00001141746chr16:50367608-50367485124BRD7_HUMAN296-337420--
1.11ENST0000039468811ENSE00001141743chr16:50362655-5036258076BRD7_HUMAN338-363260--
1.12ENST0000039468812ENSE00001141741chr16:50360302-50360195108BRD7_HUMAN363-399370--
1.13ENST0000039468813ENSE00001141735chr16:50359794-50359659136BRD7_HUMAN399-444460--
1.14ENST0000039468814ENSE00001100339chr16:50357609-50357498112BRD7_HUMAN444-481380--
1.15ENST0000039468815ENSE00001100368chr16:50355949-5035589357BRD7_HUMAN482-500190--
1.16bENST0000039468816bENSE00001141719chr16:50354685-50354574112BRD7_HUMAN501-538380--
1.17ENST0000039468817ENSE00001100356chr16:50354302-50354159144BRD7_HUMAN538-586490--
1.18ENST0000039468818ENSE00001100349chr16:50353941-50353798144BRD7_HUMAN586-634490--
1.19ENST0000039468819ENSE00001519207chr16:50353177-50352941237BRD7_HUMAN634-651180--

(-) 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:117
 aligned with BRD7_HUMAN | Q9NPI1 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:117
                                   137       147       157       167       177       187       197       207       217       227       237       
           BRD7_HUMAN   128 QEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSI 244
               SCOP domains d2i7ka_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhh...........hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------BROMODOMAIN_2  PDB: A:20-90 UniProt: 148-218                           -------------------------- PROSITE
           Transcript 1 (1) 1.4------------------Exon 1.6  PDB: A:21-69 UniProt: 149-197          Exon 1.8  PDB: A:70-106              Exon 1.9   Transcript 1 (1)
           Transcript 1 (2) --Exon 1.5  PDB: A:2-2----------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2i7k A   0 MEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERLEHHHHHH 116
                                     9        19        29        39        49        59        69        79        89        99       109       

   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  (0, 0)

(no "CATH Domain" information available for 2I7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I7K)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (BRD7_HUMAN | Q9NPI1)
molecular function
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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:0035066    positive regulation of histone acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    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:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0090544    BAF-type complex    A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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