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Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome
Biology and Chemistry Report
4JJN
  •   Structure Details   Hide

    Structure Keywords

    Keywords DNA BINDING PROTEIN/DNA
    Text BAH domain, silencing, DNA BINDING PROTEIN-DNA complex

    Polymeric Molecules

    Chain A,E
    Description Histone H3 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15260.0 
    Source Method genetically manipulated  
    Chain B,F
    Description Histone H4 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11264.3 
    Source Method genetically manipulated  
    Chain C,G
    Description Histone H2A.2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13882.1 
    Source Method genetically manipulated  
    Chain D,H
    Description Histone H2B.2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 14133.3 
    Source Method genetically manipulated  
    Chain K,L
    Description Regulatory protein SIR3 
    Mutation D205N 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 43656.0 
    Source Method genetically manipulated  
    Entity Name Silent information regulator 3 
    Chain I
    Description DNA (146-MER) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 45139.1 
    Source Method synthetic  
    Chain J
    Description DNA (146-MER) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 45610.4 
    Source Method synthetic  

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,E H3_YEAST D6VQ11     
    B,F H4_YEAST D6VQ10     
    C,G H2A2_YEAST D6VPZ9     
    D,H H2B2_YEAST D6VQ00     
    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
    6333   Chromatin Assembly or Disassembly  The Formation or Destruction of Chromatin Structures. 
    9303   RRNA Transcription  The Synthesis of Ribosomal RNA (rrna) Any RNA That Forms Part of the Ribosomal Structure From a DNA Template. 
    43935   Sexual Sporulation Resulting in Formation of a Cellular Spore  The Formation of Spores Derived From the Products of Meiosis. a Cellular Spore Is a Cell Form That Can Be Used For Dissemination For Survival of Adverse Conditions Because of Its Heat and Dessication Resistance And/or For Reproduction. 
    70911   Global Genome Nucleotide Excision Repair  The Nucleotide Excision Repair Process in Which DNA Lesions Are Removed From Nontranscribed Strands and From Transcriptionally Silent Regions Over the Entire Genome. 
    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. 
    788   Nuclear Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA in the Nucleus 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. 
    31298   Replication Fork Protection Complex  A Protein Complex Conserved in Eukaryotes and Associated with the Replication Fork; the Complex Stabilizes Stalled Replication Forks and Is Thought to Be Involved in Coordinating Leading and Lagging Strand Synthesis and in Replication Checkpoint Signaling. 
    43505   Cenp a Containing Nucleosome  A Form of Nucleosome Located Only At the Centromere in Which the Histone H3 Is Replaced by the Variant Form Cenp a (sometimes Known As Cenh3). 
    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
    6333   Chromatin Assembly or Disassembly  The Formation or Destruction of Chromatin Structures. 
    6334   Nucleosome Assembly  The Aggregation Arrangement and Bonding Together of a Nucleosome the Beadlike Structural Units of Eukaryotic Chromatin Composed of Histones and Dna. 
    34729   Histone H3 K79 Methylation  The Modification of Histone H3 by Addition of a Methyl Group to Lysine At Position 79 of the Histone. 
    43935   Sexual Sporulation Resulting in Formation of a Cellular Spore  The Formation of Spores Derived From the Products of Meiosis. a Cellular Spore Is a Cell Form That Can Be Used For Dissemination For Survival of Adverse Conditions Because of Its Heat and Dessication Resistance And/or For Reproduction. 
    61587   Transfer RNA Gene Mediated Silencing  The Chromatin Silencing That Results in the Inhibition of RNA Polymerase Ii Transcribed Genes Located in the Vicinity of TRNA Genes. 
    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. 
    788   Nuclear Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA in the Nucleus 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. 
    31298   Replication Fork Protection Complex  A Protein Complex Conserved in Eukaryotes and Associated with the Replication Fork; the Complex Stabilizes Stalled Replication Forks and Is Thought to Be Involved in Coordinating Leading and Lagging Strand Synthesis and in Replication Checkpoint Signaling. 
    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
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6333   Chromatin Assembly or Disassembly  The Formation or Destruction of Chromatin Structures. 
    6974   Cellular Response to DNA Damage 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 a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 
    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. 
    788   Nuclear Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA in the Nucleus 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. 
    31298   Replication Fork Protection Complex  A Protein Complex Conserved in Eukaryotes and Associated with the Replication Fork; the Complex Stabilizes Stalled Replication Forks and Is Thought to Be Involved in Coordinating Leading and Lagging Strand Synthesis and in Replication Checkpoint Signaling. 
    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
    6333   Chromatin Assembly or Disassembly  The Formation or Destruction of Chromatin Structures. 
    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. 
    788   Nuclear Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA in the Nucleus 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. 
    31298   Replication Fork Protection Complex  A Protein Complex Conserved in Eukaryotes and Associated with the Replication Fork; the Complex Stabilizes Stalled Replication Forks and Is Thought to Be Involved in Coordinating Leading and Lagging Strand Synthesis and in Replication Checkpoint Signaling. 
    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 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 cmt1, l9753.10, mar2, sir3, ste8, ylr442c
    Host Scientific Name Escherichia coli  
    Host Strain Rosetta De3
    Host Vector Type Plasmid
    Host Plasmid Name pET-Sumo


    Chain D,H
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene h2b2, histone h2b.2, htb2, ybl002w, ybl0104
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)


    Chain C,G
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene h2a2, histone h2a.2, hta2, ybl003c, ybl0103
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)


    Chain B,F
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene hhf1, hhf2, histone h4, n2752, ybr009c, ybr0122, ynl030w
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)


    Chain A,E
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene hht1, hht2, histone h3, n2749, sin2, ybr010w, ybr0201, ynl031c
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    II - 852295     histone H3 HHT1    
    II - 852294     histone H4 HHF1    
    II - 852283     histone H2A HTA2    
    II - 852284     histone H2B HTB2    
    XII - 851163     Sir3p SIR3    
    XIV - 855700     histone H3 HHT2    
    XIV - 855701     histone H4 HHF2