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Crystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the RXRalpha/PPARgamma heterodimer
Biology and Chemistry Report
1RDT
  •   Structure Details   Hide

    Structure Keywords

    Keywords HORMONE/GROWTH FACTOR
    Text Hormone, receptor, HORMONE-GROWTH FACTOR COMPLEX

    Polymeric Molecules

    Chain A
    Description Retinoic acid receptor RXR-alpha 
    Fragment ligand binding doamin 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 27114.6 
    Source Method genetically manipulated  
    Entity Name RXRalpha 
    Chain B
    Description LxxLL motif coactivator 
    Fragment LxxLL peptide 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 2806.2 
    Source Method synthetic  
    Chain D
    Description Peroxisome proliferator activated receptor gamma 
    Fragment ligand binding doamin 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 32558.1 
    Source Method genetically manipulated  
    Entity Name PPAR-gamma 
    Chain E
    Description LxxLL motif coactivator 
    Fragment LxxLL peptide 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 2368.7 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    570  2-(2-BENZOYL-PHENYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID  C34 H30 N2 O5   546.61  View 
    L79  (S)-(2E)-3[4-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-2-NAPHTHALENYL)TETRAHYDRO-1-BENZOFURAN-2-YL]-2-PROPENOIC ACID  C25 H30 O3   378.50  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A RXRA_HUMAN P19793     
    B NCOA1_HUMAN O00150     
    D PPARG_HUMAN A8K3G6     
    E CBP_HUMAN D3DUC9     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.3.1.48      
    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. 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 
    Chain D
    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. 
    4879   Ligand Activated Sequence Specific DNA Binding RNA Polymerase Ii Transcription Factor Activity  Combining with a Signal 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. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene pparg, nr1c3
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pRSET


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene rxra, nr2b1
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pACYC184


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p25 5468     peroxisome proliferator-activated receptor gamma PPARG    
    9 9q34.3 6256     retinoid X receptor, alpha RXRA    

    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
    rs143509964 LS-SNP   dbSNP   A 318 I - > V 3/10 Helix 24% (Intermediate) 9 137320995
    rs1805345 LS-SNP   dbSNP   A 336 S - > I Helix 28% (Intermediate) 9 137321050
    rs202174284 LS-SNP   dbSNP   A 351 T - > M Helix 52% (Exposed) 9 137323759
    rs150767145 LS-SNP   dbSNP   A 380 S - > C Bend 9% (Intermediate) 9 137325951
    rs11542209 LS-SNP   dbSNP   A 398 A - > V Helix 37% (Exposed) 9 137326005
    rs183422344 LS-SNP   dbSNP   A 406 H - > Q Helix 88% (Exposed) 9 137326030
    rs150296212 LS-SNP   dbSNP   D 212 R - > Q Helix 36% (Exposed) 3 12447480
    rs76480583 LS-SNP   dbSNP   D 238 T - > K Helix 61% (Exposed) 3 12447558
    rs200116144 LS-SNP   dbSNP   D 246 P - > L Coil 16% (Intermediate) 3 12458204
    rs147996578 LS-SNP   dbSNP   D 248 V - > I Beta Ladder 54% (Exposed) 3 12458209
    rs111400984 LS-SNP   dbSNP   D 281 I - > T Helix 12% (Intermediate) 3 12458309 570
    rs121909242 LS-SNP   dbSNP   D 286 Q - > P Helix 20% (Intermediate) 3 12458324 570
    rs28936407 LS-SNP   dbSNP   D 288 R - > H Helix 43% (Exposed) 3 12458330 570
    rs72551362 LS-SNP   dbSNP   D 290 V - > M Helix 11% (Intermediate) 3 12458335
    rs139894525 LS-SNP   dbSNP   D 307 V - > L 3/10 Helix 54% (Exposed) 3 12458386
    rs145566594 LS-SNP   dbSNP   D 328 T - > P Helix 0% (Buried) 3 12458449
    rs141683496 LS-SNP   dbSNP   D 343 E - > K Turn 85% (Exposed) 3 12458494
    rs140204299 LS-SNP   dbSNP   D 357 R - > Q Bend 38% (Exposed) 3 12458537
    rs188622140 LS-SNP   dbSNP   D 360 F - > C 3/10 Helix 12% (Intermediate) 3 12458546 570
    rs72551363 LS-SNP   dbSNP   D 360 F - > L 3/10 Helix 12% (Intermediate) 3 12458547 570
    rs148844673 LS-SNP   dbSNP   D 382 S - > R Helix 22% (Intermediate) 3 12458613
    rs72551364 LS-SNP   dbSNP   D 397 R - > C Bend 4% (Buried) 3 12475399
    rs186728157 LS-SNP   dbSNP   D 427 E - > A Turn 101% (Exposed) 3 12475490
    rs62243567 LS-SNP   dbSNP   D 449 H - > N Helix 16% (Intermediate) 3 12475555 570
    rs201781800 LS-SNP   dbSNP   D 459 T - > M Helix 44% (Exposed) 3 12475586
    rs121909244 LS-SNP   dbSNP   D 467 P - > L Helix 64% (Exposed) 3 12475610