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2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z
Biology and Chemistry Report
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  •   Structure Details   Hide

    Structure Keywords

    Keywords STRUCTURAL PROTEIN/DNA
    Text NUCLEOSOME, CHROMATIN, HISTONE, HISTONE VARIANT, PROTEIN DNA INTERACTION, NUCLEOPROTEIN, SUPERCOILED DNA, COMPLEX (NUCLEOSOME CORE-DNA), 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 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15507.3 
    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.Z 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13581.9 
    Source Method genetically manipulated  
    Chain D,H
    Description HISTONE H2B 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13979.4 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MN  MANGANESE (II) ION  Mn   54.94  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,E H32_XENLA A4FVE2     
    B,F H4_MOUSE A0AUM5     
    C,G H2AZ_HUMAN B2RD56     
    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). 
    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). 
    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. 
    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). 
    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). 
    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). 
    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). 


     
  •   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 Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name PUC


    Chain B,F
    Common Name House Mouse
    Scientific Name Mus musculus  
    Genus Mus
    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
    3 3|3 F1-F2 97122     histone cluster 2, H4 HIST2H4    
    6 6 G1|6 320332     histone cluster 4, H4 HIST4H4    
    13 13 A2-A3|13 69386     histone cluster 1, H4h HIST1H4H    
    13 13 A2-A3|13 319155     histone cluster 1, H4c HIST1H4C    
    13 13 A2-A3|13 319156     histone cluster 1, H4d HIST1H4D    
    13 13 A2-A3|13 319157     histone cluster 1, H4f HIST1H4F    
    13 13 A2-A3|13 319158     histone cluster 1, H4i HIST1H4I    
    13 13 A2-A3|13 319159     histone cluster 1, H4j HIST1H4J    
    13 13 A2-A3|13 319160     histone cluster 1, H4k HIST1H4K    
    13 13 A3.1|13 319161     histone cluster 1, H4n HIST1H4N    
    13 13 A2-A3|13 326619     histone cluster 1, H4a HIST1H4A    
    13 13 A2-A3|13 326620     histone cluster 1, H4b HIST1H4B    
    - - 446588     histone cluster 1, H2bj HIST1H2BJ    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs11554385 LS-SNP   dbSNP   C 833 H - > L Helix 19% (Intermediate) 4 100870524
    rs11554383 LS-SNP   dbSNP   C 846 V - > A Beta Ladder 11% (Intermediate) 4 100870485
    rs11554394 LS-SNP   dbSNP   C 879 K - > E Bend 80% (Exposed) 4 100870055
    rs11554386 LS-SNP   dbSNP   C 883 P - > T Helix 12% (Intermediate) 4 100870043