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Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin
Biology and Chemistry Report
1K83
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION/TOXIN
    Text TRANSCRIPTION-TOXIN COMPLEX, ALPHA AMANITIN, TOXIN, INHIBITOR, POLYMERASE, TRANSFERASE, DNA BINDING, ZINC-FINGER, PHOSPHOPROTEIN, TRANSCRIPTION, UBL TRANSCRIPTION-TOXIN COMPLEX

    Polymeric Molecules

    Chain A
    Description DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 191822.0 
    Source Method natural source  
    Entity Name RPB1 
    Chain L
    Description DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 7730.0 
    Source Method natural source  
    Entity Name RPB12 
    Chain M
    Description ALPHA AMANITIN 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 939.0 
    Source Method natural source  
    Entity Name AMATOXIN 
    Chain B
    Description DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 138938.0 
    Source Method natural source  
    Entity Name RPB2 
    Chain C
    Description DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35330.7 
    Source Method natural source  
    Entity Name RPB3 
    Chain E
    Description DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 25117.3 
    Source Method natural source  
    Entity Name RPB5 
    Chain F
    Description DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17932.0 
    Source Method natural source  
    Entity Name RPB6 
    Chain H
    Description DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 16525.5 
    Source Method natural source  
    Entity Name RPB8 
    Chain I
    Description DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 14308.2 
    Source Method natural source  
    Entity Name RPB9 
    Chain J
    Description DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 8290.8 
    Source Method natural source  
    Entity Name RPB10 
    Chain K
    Description DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13633.6 
    Source Method natural source  
    Entity Name RPB11 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MN  MANGANESE (II) ION  Mn   54.94  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A RPB1_YEAST D6VRK8     
    B RPB2_YEAST D6W2K8     
    C RPB3_YEAST D6VVQ8     
    E RPAB1_YEAST D6VQE9     
    F RPAB2_YEAST D6W4I7     
    H RPAB3_YEAST D6W2S9     
    I RPB9_YEAST D6VU72     
    J RPAB5_YEAST D6W2R6     
    K RPB11_YEAST D6W262     
    L RPAB4_YEAST D3DL93     
    M AMATX_AMAPH P85421     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    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. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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). 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain B
    GO ID   Ontology GO Term Definition
    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. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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). 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain C
    GO ID   Ontology GO Term Definition
    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. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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). 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain E
    GO ID   Ontology GO Term Definition
    42254   Ribosome Biogenesis  A Cellular Process That Results in the Biosynthesis of Constituent Macromolecules Assembly and Arrangement of Constituent Parts of Ribosome Subunits; Includes Transport to the Sites of Protein Synthesis. 
    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. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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 F
    GO ID   Ontology GO Term Definition
    42254   Ribosome Biogenesis  A Cellular Process That Results in the Biosynthesis of Constituent Macromolecules Assembly and Arrangement of Constituent Parts of Ribosome Subunits; Includes Transport to the Sites of Protein Synthesis. 
    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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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 H
    GO ID   Ontology GO Term Definition
    42254   Ribosome Biogenesis  A Cellular Process That Results in the Biosynthesis of Constituent Macromolecules Assembly and Arrangement of Constituent Parts of Ribosome Subunits; Includes Transport to the Sites of Protein Synthesis. 
    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. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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 I
    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. 
    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. 
    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. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain J
    GO ID   Ontology GO Term Definition
    42254   Ribosome Biogenesis  A Cellular Process That Results in the Biosynthesis of Constituent Macromolecules Assembly and Arrangement of Constituent Parts of Ribosome Subunits; Includes Transport to the Sites of Protein Synthesis. 
    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. 
    5730   Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Cells. It Is Rich in RNA and Protein Is Not Bounded by a Limiting Membrane and Is Not Seen During Mitosis. Its Prime Function Is the Transcription of the Nucleolar DNA Into 45s Ribosomal Precursor RNA the Processing of This RNA Into 5.8s 18s and 28s Components of Ribosomal RNA and the Association of These Components with 5s RNA and Proteins Synthesized Outside the Nucleolus. This Association Results in the Formation of Ribonucleoprotein Precursors; These Pass Into the Cytoplasm and Mature Into the 40s and 60s Subunits of the Ribosome. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain K
    GO ID   Ontology GO Term Definition
    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. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    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 L
    GO ID   Ontology GO Term Definition
    42254   Ribosome Biogenesis  A Cellular Process That Results in the Biosynthesis of Constituent Macromolecules Assembly and Arrangement of Constituent Parts of Ribosome Subunits; Includes Transport to the Sites of Protein Synthesis. 
    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. 
    5730   Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Cells. It Is Rich in RNA and Protein Is Not Bounded by a Limiting Membrane and Is Not Seen During Mitosis. Its Prime Function Is the Transcription of the Nucleolar DNA Into 45s Ribosomal Precursor RNA the Processing of This RNA Into 5.8s 18s and 28s Components of Ribosomal RNA and the Association of These Components with 5s RNA and Proteins Synthesized Outside the Nucleolus. This Association Results in the Formation of Ribonucleoprotein Precursors; These Pass Into the Cytoplasm and Mature Into the 40s and 60s Subunits of the Ribosome. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Natural Source

    Chain M
    Scientific Name Amanita phalloides  
    Chain L
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain K
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain J
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain I
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain H
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain F
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain E
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain C
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain B
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4
    Chain A
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain DELTA-RPB4

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    II - 852451     Rpb5p RPB5    
    XV - 854322     Rpb2p RPB2    
    XV - 854399     Rpb8p RPB8    
    XV - 854385     Rpb10p RPB10    
    XV - 854157     Rpb11p RPB11    
    IV - 851415     Rpo21p RPO21    
    XVI - 856317     Rpo26p RPO26    
    VII - 852810     Rpb9p RPB9    
    IX - 854791     Rpb3p RPB3    
    VIII - 856547     Rpc10p RPC10