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2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z
Biology and Chemistry Report
1F66
  •   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. 
    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
    183   Chromatin Silencing At Rdna  Repression of Transcription of Ribosomal DNA by Altering the Structure of Chromatin. 
    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. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    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 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). 
    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). 
    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. 
    Chain C,G
    GO ID   Ontology GO Term Definition
    45944   Positive Regulation of Transcription From RNA Polymerase Ii Promoter  Any Process That Activates or Increases the Frequency Rate or Extent of Transcription From an RNA Polymerase Ii Promoter. 
    71392   Cellular Response to Estradiol Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of Stimulus by Estradiol a C18 Steroid Hormone Hydroxylated At C3 and C17 That Acts As a Potent Estrogen. 
    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. 
    1740   Barr Body  A Structure Found in a Female Mammalian Cell Containing an Unpaired X Chromosome That Has Become Densely Heterochromatic Silenced and Localized At the Nuclear Periphery. 
    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. 
    5719   Nuclear Euchromatin  The Dispersed Less Dense Form of Chromatin in the Interphase Nucleus. It Exists in At Least Two Forms a Some Being in the Form of Transcriptionally Active Chromatin Which Is the Least Condensed While the Rest Is Inactive Euchromatin Which Is More Condensed Than Active Chromatin But Less Condensed Than Heterochromatin. 
    5720   Nuclear Heterochromatin  A Condensed Form of Chromatin Occurring in the Nucleus During Interphase That Stains Strongly with Basophilic Dyes. the DNA of Heterochromatin Is Typically Replicated At a Later Stage in the Cell Division Cycle Than Euchromatin. 
    70062   Extracellular 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. 
    978   RNA Polymerase Ii Core Promoter Proximal Region Sequence Specific DNA Binding  Interacting Selectively and Non Covalently with a Sequence of DNA That Is in Cis with and Relatively Close to a Core Promoter For RNA Polymerase Ii. 
    979   RNA Polymerase Ii Core Promoter Sequence Specific DNA Binding  Interacting Selectively and Non Covalently with the Regulatory Region Composed of the Transcription Start Site and Binding Sites For Transcription Factors of the RNA Polymerase Ii Basal Transcription Machinery. 
    980   RNA Polymerase Ii Distal Enhancer Sequence Specific DNA Binding  Interacting Selectively and Non Covalently with a RNA Polymerase Ii (pol Ii) Distal Enhancer. in Mammalian Cells Enhancers Are Distal Sequences That Increase the Utilization of Some Promoters and Can Function in Either Orientation and in Any Location (upstream or Downstream) Relative to the Core Promoter. 
    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). 
    31490   Chromatin DNA Binding  Interacting Selectively and Non Covalently with DNA That Is Assembled Into Chromatin. 
    31492   Nucleosomal DNA Binding  Interacting Selectively and Non Covalently with the DNA Portion of a Nucleosome. 
    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 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|6 G1 320332     histone cluster 4, H4 HIST4H4    
    13 13|13 A2-A3 69386     histone cluster 1, H4h HIST1H4H    
    13 13|13 A2-A3 319155     histone cluster 1, H4c HIST1H4C    
    13 13|13 A2-A3 319156     histone cluster 1, H4d HIST1H4D    
    13 13|13 A2-A3 319157     histone cluster 1, H4f HIST1H4F    
    13 13|13 A2-A3 319158     histone cluster 1, H4i HIST1H4I    
    13 13|13 A2-A3 319159     histone cluster 1, H4j HIST1H4J    
    13 13|13 A2-A3 319160     histone cluster 1, H4k HIST1H4K    
    13 13|13 A3.1 319161     histone cluster 1, H4n HIST1H4N    
    13 13|13 A2-A3 326619     histone cluster 1, H4a HIST1H4A    
    13 13|13 A2-A3 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