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X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
Biology and Chemistry Report
1EQZ
  •   Structure Details   Hide

    Structure Keywords

    Keywords STRUCTURAL PROTEIN/DNA
    Text NUCLEOSOME, NUCLEOSOME CORE PARTICLE, HISTONE, MICROGRAVITY HISTONE OCTAMER, DNA PALINDROME, DNA PROTEIN COMPLEX, CHROMATIN, CHROMOSOMAL PROTEIN, HISTONE FOLD, BENT DNA, STRUCTURAL PROTEIN-DNA COMPLEX

    Polymeric Molecules

    Chain I,J
    Description 146 NUCLEOTIDES LONG DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 45055.2 
    Source Method synthetic  
    Chain A,E
    Description PROTEIN (HISTONE H2A) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13969.5 
    Source Method natural source  
    Chain B,F
    Description PROTEIN (HISTONE H2B) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13953.4 
    Source Method natural source  
    Chain C,G
    Description PROTEIN (HISTONE H3) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15421.2 
    Source Method natural source  
    Chain D,H
    Description PROTEIN (HISTONE H4) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11394.5 
    Source Method natural source  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CAC  CACODYLATE ION  C2 H6 As O2   136.99  View 
    CL  CHLORIDE ION  Cl   35.45  View 
    POTASSIUM ION  K   39.10  View 
    MN  MANGANESE (II) ION  Mn   54.94  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,E H2A4_CHICK P02263     
    B,F H2B7_CHICK P02279     
    C,G H32_CHICK P02295     
    D,H H4_CHICK P02304     

    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
    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. 
    5811   Lipid Particle  An Intracellular Non Membrane Bounded Organelle Comprising a Matrix of Coalesced Lipids Surrounded by a Phospholipid Monolayer. May Include Associated Proteins. 
    35267   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). 
    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 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. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    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
    6334   Nucleosome Assembly  The Aggregation Arrangement and Bonding Together of a Nucleosome the Beadlike Structural Units of Eukaryotic Chromatin Composed of Histones and Dna. 
    6335   DNA Replication Dependent Nucleosome Assembly  The Formation of Nucleosomes On Newly Replicated DNA Coupled to Strand Elongation. 
    6336   DNA Replication Independent Nucleosome Assembly  The Formation of Nucleosomes Outside the Context of DNA Replication. 
    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. 
    45653   Negative Regulation of Megakaryocyte Differentiation  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Megakaryocyte Differentiation. 
    228   Nuclear Chromosome  A Chromosome Found in the Nucleus of a Eukaryotic Cell. 
    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. 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 


     
  •   Gene Details   Hide

    Natural Source

    Chain D,H
    Common Name Chicken
    Scientific Name Gallus gallus  
    Genus Gallus
    Organelle Erythrocyte Nucleus
    Tissue Blood
    Chain C,G
    Common Name Chicken
    Scientific Name Gallus gallus  
    Genus Gallus
    Organelle Erythrocyte Nucleus
    Tissue Blood
    Chain B,F
    Common Name Chicken
    Scientific Name Gallus gallus  
    Genus Gallus
    Organelle Erythrocyte Nucleus
    Tissue Blood
    Chain A,E
    Common Name Chicken
    Scientific Name Gallus gallus  
    Genus Gallus
    Organelle Erythrocyte Nucleus
    Tissue Blood

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 - 404299     histone cluster 1, H2A, IV (similar to human histone cluster 2, class H2A, member C) HIST1H2A4    
    1 - 417950     histone cluster 1, histone class H4, member 7 (similar to human histone cluster 1, class H4 genes) HIST1H47    
    3 - 427887     H3 histone, family 3C H3F3C