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(-) Description

Title :  DROSOPHILA MSL3 CHROMODOMAIN
 
Authors :  D. Kim, P. Huang, F. Rastinejad, S. Khorasanizadeh
Date :  22 Mar 10  (Deposition) - 21 Jul 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chromodomain, Msl3, Methyllysine Recognition, Aromatic Cage, Msl Complex, Transcription Upregulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Kim, B. J. Blus, V. Chandra, P. Huang, F. Rastinejad, S. Khorasanizadeh
Corecognition Of Dna And A Methylated Histone Tail By The Msl3 Chromodomain.
Nat. Struct. Mol. Biol. V. 17 1027 2010
PubMed-ID: 20657587  |  Reference-DOI: 10.1038/NSMB.1856

(-) Compounds

Molecule 1 - PROTEIN MALE-SPECIFIC LETHAL-3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMSL-3, CG8631
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3M9Q)

(-) Sites  (0, 0)

(no "Site" information available for 3M9Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M9Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M9Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M9Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M9Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3M9Q)

(-) Sequences/Alignments

Asymmetric 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:89
 aligned with MSL3_DROME | P50536 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:89
                                    13        23        33        43        53        63        73        83         
            MSL3_DROME    4 LRDETPLFHKGEIVLCYEPDKSKARVLYTSKVLNVFERRNEHGLRFYEYKIHFQGWRPSYDRCVRATVLLKDTEENRQLQRELAEAAKL 92
               SCOP domains d3m9qa_ A: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeehhh.eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3m9q A  4 LRDETPLFHKGEIVLCYEPDKSKARVLYTSKVLNVFERRNEHGLRFYEYKIHFQGWRPSYDRAVRATVLLKDTEENRQLQRELAEAAKL 92
                                    13        23        33        43        53        63        73        83         

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with MSL3_DROME | P50536 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:87
                                    13        23        33        43        53        63        73        83       
            MSL3_DROME    4 LRDETPLFHKGEIVLCYEPDKSKARVLYTSKVLNVFERRNEHGLRFYEYKIHFQGWRPSYDRCVRATVLLKDTEENRQLQRELAEAA 90
               SCOP domains d3m9qb_ B: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeehhh.eee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  3m9q B  4 LRDETPLFHKGEIVLCYEPDKSKARVLYTSKVLNVFERRNEHGLRFYEYKIHFQGWRPSYDRAVRATVLLKDTEENRQLQRELAEAA 90
                                    13        23        33        43        53        63        73        83       

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M9Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M9Q)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MSL3_DROME | P50536)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
biological process
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0007549    dosage compensation    Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes.
    GO:0009047    dosage compensation by hyperactivation of X chromosome    Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global hyperactivation of all, or most of, the genes on the X-chromosome in the heterogametic sex, leading to a two-fold increase in gene expression from this chromosome. An example of this is found in Drosophila melanogaster.
    GO:0043968    histone H2A acetylation    The modification of histone H2A by the addition of an acetyl group.
    GO:0043967    histone H4 acetylation    The modification of histone H4 by the addition of an acetyl group.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0031936    negative regulation of chromatin silencing    Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing.
    GO:0035206    regulation of hemocyte proliferation    Any process that modulates the frequency, rate or extent of hemocyte proliferation. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen. An example of this is found in Drosophila melanogaster.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0072487    MSL complex    A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residue at position 16. In human, it contains the catalytic subunit MOF, and MSL1, MSL2 and MSL3.
    GO:0035267    NuA4 histone acetyltransferase complex    A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
    GO:0000805    X chromosome    The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males.
    GO:0016456    X chromosome located dosage compensation complex, transcription activating    An RNA-protein complex localized to the X chromosome of males where it is required for the hyper-transcriptional activation of the X chromosome. An example of this is found in Drosophila melanogaster.
    GO:0010369    chromocenter    A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    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:0005700    polytene chromosome    A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible.

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3m9p