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Revealing a marine natural product as a novel agonist for retinoic acid receptors with a unique binding mode and antitumor activity
Biology and Chemistry Report
4DQM
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION/TRANSFERASE
    Text nuclear receptor transcription factor, ligand binding domain, Transcription regulation, Nucleus, TRANSCRIPTION-TRANSFERASE complex

    Polymeric Molecules

    Chain A,C
    Description Retinoic acid receptor alpha 
    Fragment ligand binding domain, UNP RESIDUES 182-415 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 26486.1 
    Source Method genetically manipulated  
    Entity Name RAR-alpha, Nuclear receptor subfamily 1 group B member 1 
    Chain B,D
    Description Nuclear receptor coactivator 1 
    Fragment LXXLL motif 7, UNP RESIDUES 1432-1441 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1173.4 
    Source Method synthetic  
    Entity Name NCoA-1, Class E basic helix-loop-helix protein 74, bHLHe74, Protein Hin-2, RIP160, Renal carcinoma antigen NY-REN-52, Steroid receptor coactivator 1, SRC-1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    LUF  (5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethylcyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxyfuran-2(5H)-one  C25 H38 O3   386.57  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C RARA_HUMAN B8Y636     
    B,D NCOA1_HUMAN O00150     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    B D  2.3.1.48      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    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. 
    48384   Retinoic Acid Receptor Signaling Pathway  The Series of Molecular Signals Generated As a Consequence of a Retinoic Acid Receptor Binding to One of Its Physiological Ligands. 
    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. 
    3708   Retinoic Acid Receptor Activity  Combining with Retinoic Acid 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. Retinoic Acid Is One of the Forms of Vitamin A. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Gene nr1b1, rara
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET24a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2p23 8648     nuclear receptor coactivator 1 NCOA1    
    17 17q21 5914     retinoic acid receptor, alpha RARA    

    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
    rs79997555 LS-SNP   dbSNP   A 186 E - > G Helix 54% (Exposed) 17 38508249
    rs79997555 LS-SNP   dbSNP   A 186 E - > G Helix 54% (Exposed) 17 38508249
    rs112626578 LS-SNP   dbSNP   A 187 L - > P Helix 13% (Intermediate) 17 38508252
    rs112626578 LS-SNP   dbSNP   A 187 L - > P Helix 13% (Intermediate) 17 38508252
    rs201919660 LS-SNP   dbSNP   A 225 W - > R Helix 10% (Intermediate) 17 38508625 NULL
    rs201919660 LS-SNP   dbSNP   A 225 W - > R Helix 10% (Intermediate) 17 38508625 NULL
    rs200827868 LS-SNP   dbSNP   A 248 G - > D Turn 27% (Intermediate) 17 38508695
    rs200827868 LS-SNP   dbSNP   A 248 G - > D Turn 27% (Intermediate) 17 38508695
    rs145829003 LS-SNP   dbSNP   A 318 P - > R 3/10 Helix 71% (Exposed) 17 38510699
    rs145829003 LS-SNP   dbSNP   A 318 P - > R 3/10 Helix 71% (Exposed) 17 38510699
    rs148999974 LS-SNP   dbSNP   A 323 D - > E Helix 23% (Intermediate) 17 38510715
    rs148999974 LS-SNP   dbSNP   A 323 D - > E Helix 23% (Intermediate) 17 38510715