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THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND ROSIGLITAZONE AND CO-ACTIVATOR PEPTIDES.
Biology and Chemistry Report
1FM6
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION
    Text the heterodimer of the nuclear receptor ligand binding domains of RXRalpha and PPARgamma bound respectively with 9-cis Retinoic Acid and Rosiglitazone and co-activator peptides, TRANSCRIPTION

    Polymeric Molecules

    Chain A,U
    Description RETINOIC ACID RECEPTOR RXR-ALPHA 
    Fragment LIGAND BINDING DOMAIN - RESIDUES 225 -462 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 26668.0 
    Source Method genetically manipulated  
    Chain D,X
    Description PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA 
    Fragment LIGAND BINDING DOMAIN - RESIDUES 206 - 477 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 31094.4 
    Source Method genetically manipulated  
    Chain B,E,V,Y
    Description STEROID RECEPTOR COACTIVATOR 
    Fragment SRC-1 PEPTIDE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 2806.2 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    9CR  (9cis)-retinoic acid  C20 H28 O2   300.44  View 
    BRL  2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)  C18 H19 N3 O3 S   357.43  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,U RXRA_HUMAN P19793     
    B,E,V,Y NCOA1_HUMAN O00150     
    D,X PPARG_HUMAN A8K3G6     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    B E V Y  2.3.1.48      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,U
    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,X
    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,X
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    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,U
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    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
    rs141477822 LS-SNP   dbSNP   A 247 E - > K Bend 42% (Exposed) 9 137309132
    rs61751479 LS-SNP   dbSNP   A 254 M - > I Turn 44% (Exposed) 9 137309155
    rs145832863 LS-SNP   dbSNP   A 260 S - > L Coil 51% (Exposed) 9 137309172
    rs2234960 LS-SNP   dbSNP   A 261 P - > L Coil 45% (Exposed) 9 137313523
    rs143509964 LS-SNP   dbSNP   A 318 I - > V Turn 22% (Intermediate) 9 137320995
    rs1805345 LS-SNP   dbSNP   A 336 S - > I Helix 30% (Intermediate) 9 137321050
    rs202174284 LS-SNP   dbSNP   A 351 T - > M Helix 56% (Exposed) 9 137323759
    rs150767145 LS-SNP   dbSNP   A 380 S - > C Bend 6% (Buried) 9 137325951
    rs11542209 LS-SNP   dbSNP   A 398 A - > V Helix 39% (Exposed) 9 137326005
    rs183422344 LS-SNP   dbSNP   A 406 H - > Q Helix 89% (Exposed) 9 137326030
    rs150296212 LS-SNP   dbSNP   D 212 R - > Q Helix 35% (Intermediate) 3 12447480
    rs76480583 LS-SNP   dbSNP   D 238 T - > K Helix 75% (Exposed) 3 12447558
    rs200116144 LS-SNP   dbSNP   D 246 P - > L Coil 18% (Intermediate) 3 12458204
    rs147996578 LS-SNP   dbSNP   D 248 V - > I Beta Ladder 46% (Exposed) 3 12458209
    rs111400984 LS-SNP   dbSNP   D 281 I - > T Helix 6% (Buried) 3 12458309 BRL
    rs121909242 LS-SNP   dbSNP   D 286 Q - > P Helix 6% (Buried) 3 12458324 BRL
    rs28936407 LS-SNP   dbSNP   D 288 R - > H Helix 41% (Exposed) 3 12458330 BRL
    rs72551362 LS-SNP   dbSNP   D 290 V - > M Helix 8% (Buried) 3 12458335
    rs139894525 LS-SNP   dbSNP   D 307 V - > L Turn 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 3/10 Helix 62% (Exposed) 3 12458494
    rs140204299 LS-SNP   dbSNP   D 357 R - > Q Bend 26% (Intermediate) 3 12458537
    rs188622140 LS-SNP   dbSNP   D 360 F - > C 3/10 Helix 1% (Buried) 3 12458546
    rs72551363 LS-SNP   dbSNP   D 360 F - > L 3/10 Helix 1% (Buried) 3 12458547
    rs148844673 LS-SNP   dbSNP   D 382 S - > R Helix 24% (Intermediate) 3 12458613
    rs72551364 LS-SNP   dbSNP   D 397 R - > C Bend 2% (Buried) 3 12475399
    rs186728157 LS-SNP   dbSNP   D 427 E - > A Turn 97% (Exposed) 3 12475490
    rs62243567 LS-SNP   dbSNP   D 449 H - > N Helix 10% (Intermediate) 3 12475555 BRL
    rs201781800 LS-SNP   dbSNP   D 459 T - > M Helix 57% (Exposed) 3 12475586
    rs121909244 LS-SNP   dbSNP   D 467 P - > L Helix 58% (Exposed) 3 12475610