POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
Biology and Chemistry Report
1M19
  •   Structure Details   Hide

    Structure Keywords

    Keywords STRUCTURAL PROTEIN/DNA
    Text nucleosome, chromatin, histone, pyrrole-imidazole polyamide, DNA regognition, chromatin remodeling, STRUCTURAL PROTEIN-DNA COMPLEX

    Polymeric Molecules

    Chain I,J
    Description Palindromic 146 Base Pair DNA Fragment 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 45055.2 
    Source Method synthetic  
    Chain A,E
    Description Histone H3.2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15320.2 
    Source Method genetically manipulated  
    Chain B,F
    Description Histone H4 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11263.3 
    Source Method genetically manipulated  
    Chain C,G
    Description Histone H2A.1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13962.4 
    Source Method genetically manipulated  
    Chain D,H
    Description Histone H2B.1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13848.2 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ABU  GAMMA-AMINO-BUTANOIC ACID  C4 H9 N O2   103.12  View 
    BAL  BETA-ALANINE  C3 H7 N O2   89.09  View 
    DIB  3-AMINO-(DIMETHYLPROPYLAMINE)  C5 H14 N2   102.18  View 
    IMT  4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID  C5 H7 N3 O2   141.13  View 
    MN  MANGANESE (II) ION  Mn   54.94  View 
    PYB  4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID  C6 H8 N2 O2   140.14  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,E H3C_XENLA P02302     
    B,F H4_XENLA P02304     
    C,G H2A1_XENLA P06897     
    D,H H2B11_XENLA P02281     

    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. 
    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 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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain D,H
    Common Name African Clawed Frog
    Scientific Name Xenopus laevis  
    Genus Xenopus
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name PET


    Chain C,G
    Common Name African Clawed Frog
    Scientific Name Xenopus laevis  
    Genus Xenopus
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name PET


    Chain B,F
    Common Name African Clawed Frog
    Scientific Name Xenopus laevis  
    Genus Xenopus
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name PET


    Chain A,E
    Common Name African Clawed Frog
    Scientific Name Xenopus laevis  
    Genus Xenopus
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name PET


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 734746     H2A histone family, member X H2AFX    
    - - 446588     histone cluster 1, H2bj HIST1H2BJ