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Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide
Biology and Chemistry Report
2HCD
  •   Structure Details   Hide

    Structure Keywords

    Keywords GENE REGULATION
    Text alpha helical sandwich, GENE REGULATION

    Polymeric Molecules

    Chain A
    Description Vitamin D receptor 
    Fragment Ligand binding domain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34060.9 
    Source Method genetically manipulated  
    Chain B
    Description SRC-1 from Nuclear receptor coactivator 1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1776.1 
    Source Method synthetic  
    Entity Name NCoA-1, Steroid receptor coactivator 1, SRC-1, RIP160, Protein Hin-2, NY-REN-52 antigen 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    BIV  21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E)  C32 H54 O4   502.77  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A VDRA_DANRE Q9PTN2     
    B NCOA1_HUMAN Q15788     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.3.1.48      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    43401   Steroid Hormone Mediated Signaling Pathway  A Series of Molecular Signals Mediated by a Steroid Hormone Binding to a Receptor. 
    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). 
    3700   Sequence Specific DNA Binding Transcription Factor Activity  Interacting Selectively and Non Covalently with a Specific DNA Sequence in Order to Modulate Transcription. the Transcription Factor May or May Not Also Interact Selectively with a Protein or Macromolecular Complex. 
    3707   Steroid Hormone Receptor Activity  Combining with a Steroid Hormone and Transmitting the Signal Within the Cell to Initiate a Change in Cell Activity or Function. 
    8434   Calcitriol Receptor Activity  Combining with Calcitriol the Hormonally Active Form of Vitamin D3 and Transmitting the Signal to the Transcriptional Machinery by Interacting Selectively and Non Covalently with a Specific DNA Sequence in Order to Modulate Transcription by RNA Polymerase Ii. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Zebrafish
    Scientific Name Danio rerio  
    Genus Danio
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21de3
    Host Vector Type Plasmid
    Host Plasmid Name pET28b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2p23 8648     nuclear receptor coactivator 1 NCOA1    
    23 - 30076     vitamin D (1,25- dihydroxyvitamin D3) receptor a VDRA