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(-) Description

Title :  SOLUTION STRUCTURE OF THE INTERDIGITATED DOUBLE TUDOR DOMAIN OF RBBP1
 
Authors :  W. Gong, Y. Feng
Date :  15 Jul 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Retinoblastoma Binding Protein 1, Interdigitated Double Tudor Domain, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Gong, J. Wang, S. Perrett, Y. Feng
Retinoblastoma-Binding Protein 1 Has An Interdigitated Double Tudor Domain With Dna-Binding Activity.
J. Biol. Chem. 2013
PubMed-ID: 24379399  |  Reference-DOI: 10.1074/JBC.M113.501940

(-) Compounds

Molecule 1 - AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 4A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGBO
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 4-121
    Gene: ARID4A, RBBP1, RBP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARID DOMAIN-CONTAINING PROTEIN 4A, RETINOBLASTOMA-BINDING PROTEIN 1, RBBP-1

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MAM)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:118
 aligned with ARI4A_HUMAN | P29374 from UniProtKB/Swiss-Prot  Length:1257

    Alignment length:118
                                    13        23        33        43        53        63        73        83        93       103       113        
          ARI4A_HUMAN     4 ADEPAYLTVGTDVSAKYRGAFCEAKIKTVKRLVKVKVLLKQDNTTQLVQDDQVKGPLRVGAIVETRTSDGSFQEAIISKLTDASWYTVVFDDGDERTLRRTSLCLKGERHFAESETLD 121
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..eeeeeeeeeeeeeeeeeeee.....eeeee...ee.......eeeee.....eeeeeeeeeeeeeeeeeee....eeeee.hhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2mam A   1 ADEPAYLTVGTDVSAKYRGAFCEAKIKTVKRLVKVKVLLKQDNTTQLVQDDQVKGPLRVGAIVETRTSDGSFQEAIISKLTDASWYTVVFDDGDERTLRRTSLCLKGERHFAESETLD 118
                                    10        20        30        40        50        60        70        80        90       100       110
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  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 2MAM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P29374: 2lcc 2yrv

(-) Related Entries Specified in the PDB File

2lcc NMR STRUCTURE OF RBBP1 CHROMOBARREL DOMAIN RELATED ID: 17607 RELATED DB: BMRB