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An Information Portal to 107049 Biological Macromolecular Structures

Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle
Biology and Chemistry Report
4LD9
  •   Structure Details   Hide

    Structure Keywords

    Keywords NUCLEAR PROTEIN/TRANSCRIPTION/DNA
    Text BETA BARREL, PROTEIN-DNA COMPLEX, DOUBLE HELIX, alpha-helix, beta-sheet, double stranded DNA, chromatin binding, chromatin, N-terminal acetylation, nucleus, NUCLEAR PROTEIN-TRANSCRIPTION-DNA complex

    Polymeric Molecules

    Chain A,E
    Description Histone H3.2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15421.2 
    Source Method genetically manipulated  
    Chain B,F
    Description Histone H4 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11394.5 
    Source Method genetically manipulated  
    Chain C,G
    Description Histone H2A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 14109.6 
    Source Method genetically manipulated  
    Chain D,H
    Description Histone H2B 1.1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13965.4 
    Source Method genetically manipulated  
    Entity Name H2B1.1 
    Chain I
    Description Widom 601 sequence reverse 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 51809.4 
    Source Method synthetic  
    Chain J
    Description Widom 601 sequence forward 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 51342.1 
    Source Method synthetic  
    Chain K,L
    Description Regulatory protein SIR3 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 28074.1 
    Source Method genetically manipulated  
    Entity Name Silent information regulator 3 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,E H32_XENLA A4FVE2     
    B,F H4_XENLA P02304     
    C,G H2A1_XENLA P06897     
    D,H H2B11_XENLA P02281     
    K,L SIR3_YEAST D6VZ77     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,E
    GO ID   Ontology GO Term Definition
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    5634   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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    5515   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). 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain B,F
    GO ID   Ontology GO Term Definition
    6334   Nucleosome Assembly  The Aggregation Arrangement and Bonding Together of a Nucleosome the Beadlike Structural Units of Eukaryotic Chromatin Composed of Histones and Dna. 
    6352   DNA Templated Transcription Initiation  Any Process Involved in the Assembly of the RNA Polymerase Preinitiation Complex (pic) At the Core Promoter Region of a DNA Template Resulting in the Subsequent Synthesis of RNA From That Promoter. the Initiation Phase Includes Pic Assembly and the Formation of the First Few Bonds in the RNA Chain Including Abortive Initiation Which Occurs When the First Few Nucleotides Are Repeatedly Synthesized and Then Released. the Initiation Phase Ends Just Before and Does Not Include Promoter Clearance or Release Which Is the Transition Between the Initiation and Elongation Phases of Transcription. 
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    5634   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. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    5515   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). 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain C,G
    GO ID   Ontology GO Term Definition
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    5634   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. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain D,H
    GO ID   Ontology GO Term Definition
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    5634   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. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain K,L
    GO ID   Ontology GO Term Definition
    3682   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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain K,L
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene sir3, cmt1, mar2, ste8, ylr442c, l9753.10
    Host Scientific Name Spodoptera frugiperda  


    Chain D,H
    Common Name Clawed Frog Common Platanna Platanna
    Scientific Name Xenopus laevis  
    Host Scientific Name Escherichia coli  


    Chain C,G
    Common Name Clawed Frog Common Platanna Platanna
    Scientific Name Xenopus laevis  
    Gene loc494591
    Host Scientific Name Escherichia coli  


    Chain B,F
    Common Name Clawed Frog Common Platanna Platanna
    Scientific Name Xenopus laevis  
    Host Scientific Name Escherichia coli  


    Chain A,E
    Common Name Clawed Frog Common Platanna Platanna
    Scientific Name Xenopus laevis  
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 100049126     histone cluster 2, H3c HIST2H3C    
    - - 447787     histone cluster 1, H4a HIST1H4A    
    - - 446588     histone cluster 1, H2bj HIST1H2BJ    
    XII - 851163     chromatin-silencing protein SIR3 SIR3