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(-) Description

Title :  ISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR HRAR: THE COMPLEX WITH THE RARGAMMA-SELECTIVE RETINOID BMS184394
 
Authors :  B. P. Klaholz, A. Mitschler, D. Moras, Structural Proteomics In Europe (Spine)
Date :  19 Jul 00  (Deposition) - 11 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A
Keywords :  Isotype Selectivity, Retinoid Ligand Complexes, Drug Design, Antiparallel Alpha-Helical Sandwich Fold, Structural Proteomics In Europe, Spine, Structural Genomics, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. P. Klaholz, A. Mitschler, D. Moras
Structural Basis For Isotype Selectivity Of The Human Retinoic Acid Nuclear Receptor.
J. Mol. Biol. V. 302 155 2000
PubMed-ID: 10964567  |  Reference-DOI: 10.1006/JMBI.2000.4032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR GAMMA-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCOMPLEXED WITH BMS184394, RESIDUE 184

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
11841Ligand/Ion6-[HYDROXY-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTALEN-2-YL)-METHYL]-NAPHTALENE-2-CARBOXYLIC ACID
2LMU1Ligand/IonDODECYL-ALPHA-D-MALTOSIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:201 , PHE A:230 , CYS A:237 , LEU A:271 , MET A:272 , ILE A:275 , PHE A:288 , SER A:289 , GLY A:303 , LEU A:400 , ILE A:412 , HOH A:548BINDING SITE FOR RESIDUE 184 A 450
2AC2SOFTWARELYS A:236 , LYS A:240 , GLU A:243 , CYS A:267 , ASP A:340 , GLN A:354 , PRO A:377 , LEU A:380 , ILE A:383 , THR A:384 , ARG A:387 , HOH A:560 , HOH A:605 , HOH A:645 , HOH A:675 , HOH A:719BINDING SITE FOR RESIDUE LMU A 451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FCX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FCX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FCX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FCX)

(-) Exons   (0, 0)

(no "Exon" information available for 1FCX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:235
 aligned with RARG_HUMAN | P13631 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:235
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412     
           RARG_HUMAN   183 SPQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE 417
               SCOP domains d1fcxa_ A: Retinoic acid receptor gamma (RAR-gamma)                                                                                                                                                                                         SCOP domains
               CATH domains 1fcxA00 A:183-417 Retinoid X Receptor                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fcx A 183 SPQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE 417
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FCX)

(-) Gene Ontology  (61, 61)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RARG_HUMAN | P13631)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    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).
    GO:0003708    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.
    GO:0046965    retinoid X receptor binding    Interacting selectively and non-covalently with a retinoid X receptor.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    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.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0070384    Harderian gland development    The process whose specific outcome is the progression of the Harderian gland over time, from its formation to the mature structure. The Harderian gland is an anterior orbital structure usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0060348    bone development    The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
    GO:0060349    bone morphogenesis    The process in which bones are generated and organized.
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0071300    cellular response to retinoic acid    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 retinoic acid stimulus.
    GO:0002063    chondrocyte development    The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
    GO:0031076    embryonic camera-type eye development    The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure.
    GO:0048048    embryonic eye morphogenesis    The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
    GO:0035116    embryonic hindlimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
    GO:0060429    epithelium development    The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
    GO:0060324    face development    The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
    GO:0048732    gland development    The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion.
    GO:0002068    glandular epithelial cell development    The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
    GO:0003430    growth plate cartilage chondrocyte growth    The growth of a growth plate cartilage chondrocyte, where growth contributes to the progression of the chondrocyte over time from one condition to another.
    GO:0003417    growth plate cartilage development    The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
    GO:0060173    limb development    The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0061037    negative regulation of cartilage development    Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0045596    negative regulation of cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0032331    negative regulation of chondrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0043068    positive regulation of programmed cell death    Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0060740    prostate gland epithelium morphogenesis    The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
    GO:0008361    regulation of cell size    Any process that modulates the size of a cell.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0031641    regulation of myelination    Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0045637    regulation of myeloid cell differentiation    Any process that modulates the frequency, rate or extent of myeloid cell differentiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048608    reproductive structure development    The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    GO:0003406    retinal pigment epithelium development    The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells.
    GO:0048384    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.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0060534    trachea cartilage development    The process whose specific outcome is the progression of the tracheal cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RARG_HUMAN | P136311exa 1exx 1fcy 1fcz 1fd0 2lbd 3lbd 4lbd

(-) Related Entries Specified in the PDB File

1exa CONTAINS THE SAME PROTEIN COMPLEXED WITH THE RETINOID BMS270394
1exx CONTAINS THE SAME PROTEIN COMPLEXED WITH THE RETINOID BMS270395
1fcy CONTAINS THE SAME PROTEIN COMPLEXED WITH THE RETINOID CD564
1fcz CONTAINS THE SAME PROTEIN COMPLEXED WITH THE RETINOID BMS181156
1fd0 CONTAINS THE SAME PROTEIN COMPLEXED WITH THE RETINOID SR11254 RELATED ID: IGBMC-0078-000 RELATED DB: TARGETDB
2lbd CONTAINS THE SAME PROTEIN COMPLEXED WITH ALL-TRANS RETINOIC ACID
3lbd CONTAINS THE SAME PROTEIN COMPLEXED WITH 9-CIS RETINOIC ACID