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(-) Description

Title :  SOLUTION STRUCTURE OF THE RBB1NT DOMAIN OF HUMAN RB(RETINOBLASTOMA)-BINDING PROTEIN 1
 
Authors :  N. Nameki, K. Saito, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Arid Domain-Containing Protein 4A, Retinoblastoma-Binding Protein 1, Rbbp-1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Nameki, K. Saito, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of The Rbb1Nt Domain Of Human Rb(Retinoblastoma)-Binding Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 4A
    ChainsA
    EngineeredYES
    Expression System PlasmidP051025-08
    Expression System Vector TypePLASMID
    FragmentUNP REGION 170-273
    GeneARID4A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymARID DOMAIN-CONTAINING PROTEIN 4A, RETINOBLASTOMA- BINDING PROTEIN 1, RBBP-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 2YRV)

(-) Sites  (0, 0)

(no "Site" information available for 2YRV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YRV)

(-) Exons   (0, 0)

(no "Exon" information available for 2YRV)

(-) 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 ARI4A_HUMAN | P29374 from UniProtKB/Swiss-Prot  Length:1257

    Alignment length:155
                                   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281     
          ARI4A_HUMAN   132 GTPVIAKKTNRGRRSSLPVTEDEKEEESSEEEDEDKRRLNDELLGKVVSVVSATERTEWYPALVISPSCNDDITVKKDQCLVRSFIDSKFYSIARKDIKEVDILNLPESELSTKPGLQKASIFLKTRVVPDNWKMDISEILESSSSDDEDGPAEE 286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------RBB1NT-2yrvA01 A:8-101                                                                        ----------------------- Pfam domains
         Sec.struct. author ..--------..---------------..--------.........eeeee.......eeeeeee..............eeeee.....eeee....ee.......hhhhhhhhhhhhhhhhhhhh..........hhhhhh.-------..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yrv A   1 GS--------SG---------------SS--------GLNDELLGKVVSVVSATERTEWYPALVISPSCNDDITVKKDQCLVRSFIDSKFYSIARKDIKEVDILNLPESELSTKPGLQKASIFLKTRVVPDNWKMDISEILES-------GPSSG 117
                             |       -||       -       ||-       | 9        19        29        39        49        59        69        79        89        99       109  |      -|    
                             2        3|               5|        7                                                                                                      112     113    
                                       4                6                                                                                                                              

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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 2YRV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (ARI4A_HUMAN | P29374)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0048821    erythrocyte development    The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
    GO:0097368    establishment of Sertoli cell barrier    Establishment of a structure near the basement membrane in adjacent Sertoli cells of the seminiferous epithelium for maintaining spermatogenesis. The structure consists of tight junctions, basal ectoplasmic specializations, and desmosome-like junctions.
    GO:0080182    histone H3-K4 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
    GO:0036124    histone H3-K9 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 9 of the histone.
    GO:0034773    histone H4-K20 trimethylation    The modification of histone H4 by addition of three methyl groups to lysine at position 20 of the histone.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    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:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006349    regulation of gene expression by genetic imprinting    Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.
    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:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    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.
    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
        ARI4A_HUMAN | P293742lcc 2mam

(-) Related Entries Specified in the PDB File

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