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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE RETINOID X RECEPTOR ALPHA IN COMPLEX WITH 3-(2'-METHOXY)-TETRAHYDRONAPHTYL CINNAMIC ACID AND A FRAGMENT OF THE COACTIVATOR TIF-2
 
Authors :  W. Bourguet, V. Nahoum
Date :  06 Mar 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protein-Ligand Complex, Hormone Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Nahoum, E. Perez, P. Germain, F. Rodriguez-Barrios, F. Manzo, S. Kammerer, G. Lemaire, O. Hirsch, C. A. Royer, H. Gronemeyer, A. R. De Lera, W. Bourguet
Modulators Of The Structural Dynamics Of The Retinoid X Receptor To Reveal Receptor Function.
Proc. Natl. Acad. Sci. Usa V. 104 17323 2007
PubMed-ID: 17947383  |  Reference-DOI: 10.1073/PNAS.0705356104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR RXR-ALPHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN (RESIDUES 223-462)
    GeneRXRA, NR2B1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRETINOID X RECEPTOR ALPHA
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 2 PEPTIDE
    ChainsB
    EngineeredYES
    FragmentNUCLEAR RECEPTOR INTERACTION MOTIF 2 (RESIDUES 686-698)
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS. THE PEPTIDE HAS BEEN SYNTHESIZED BY AUTOMATIC CHEMICAL SYNTHESIS.
    SynonymNCOA-2, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
13TN1Ligand/Ion(2E)-3-[4-HYDROXY-3-(3-METHOXY-5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PHENYL]ACRYLIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13TN2Ligand/Ion(2E)-3-[4-HYDROXY-3-(3-METHOXY-5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PHENYL]ACRYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:268 , CYS A:269 , ALA A:271 , ALA A:272 , GLN A:275 , ASN A:306 , LEU A:309 , PHE A:313 , ARG A:316 , ILE A:324 , LEU A:326 , ALA A:327 , ILE A:345 , HIS A:435 , HOH A:480 , HOH A:555BINDING SITE FOR RESIDUE 3TN A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P1T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050582A327SRXRA_HUMANPolymorphism1805345AA327S
2UniProtVAR_014621S336IRXRA_HUMANPolymorphism1805345AS336I
3UniProtVAR_050583A398VRXRA_HUMANPolymorphism11542209AA398V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050582A327SRXRA_HUMANPolymorphism1805345AA327S
2UniProtVAR_014621S336IRXRA_HUMANPolymorphism1805345AS336I
3UniProtVAR_050583A398VRXRA_HUMANPolymorphism11542209AA398V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P1T)

(-) Exons   (0, 0)

(no "Exon" information available for 2P1T)

(-) Sequences/Alignments

Asymmetric 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:211
 aligned with RXRA_HUMAN | P19793 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:230
                                   238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458
           RXRA_HUMAN   229 DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP 458
               SCOP domains d2p1ta_ A: Reti                   noid-X receptor alpha (RXR-alpha)                                                                                                                                                                    SCOP domains
               CATH domains 2p1tA00 A:229-4                   58 Retinoid X Receptor                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh-------------------hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeehhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------S--------I-------------------------------------------------------------V------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1t A 229 DMPVERILEAELAVE-------------------DPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP 458
                                   238    |    -         -    |  268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458
                                        243                 263                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:10
 aligned with NCOA2_HUMAN | Q15596 from UniProtKB/Swiss-Prot  Length:1464

    Alignment length:10
                                   696
          NCOA2_HUMAN   687 HKILHRLLQD 696
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2p1t B 687 HKILHRLLQD 696
                                   696

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P1T)

(-) Gene Ontology  (119, 132)

Asymmetric Unit(hide GO term definitions)
Chain A   (RXRA_HUMAN | P19793)
molecular function
    GO:0004886    9-cis retinoic acid receptor activity    Combining with 9-cis 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.
    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:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    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.
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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:0042974    retinoic acid receptor binding    Interacting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily.
    GO:0044323    retinoic acid-responsive element binding    Interacting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0042809    vitamin D receptor binding    Interacting selectively and non-covalently with the vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes.
    GO:0070644    vitamin D response element binding    Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031103    axon regeneration    The regrowth of axons following their loss or damage.
    GO:0015721    bile acid and bile salt transport    The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0060038    cardiac muscle cell proliferation    The expansion of a cardiac muscle cell population by cell division.
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:0032869    cellular response to insulin stimulus    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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0001893    maternal placenta development    Maternally driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0007494    midgut development    The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.
    GO:0019048    modulation by virus of host morphology or physiology    The process in which a virus effects a change in the structure or processes of its host organism.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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:0035357    peroxisome proliferator activated receptor signaling pathway    The series of molecular signals initiated by binding of a ligand to any of the peroxisome proliferator activated receptors (alpha, beta or gamma) in the nuclear membrane, and ending with the initiation or termination of the transcription of target genes.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    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: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:1901522    positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus    Any positive regulation of transcription from RNA polymerase II promoter that is involved in cellular response to chemical stimulus.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045994    positive regulation of translational initiation by iron    Any process involving iron that activates or increases the rate of translational initiation.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0060687    regulation of branching involved in prostate gland morphogenesis    Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045471    response to ethanol    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 an ethanol stimulus.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0007584    response to nutrient    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 nutrient stimulus.
    GO:0014070    response to organic cyclic compound    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 an organic cyclic compound stimulus.
    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:0010269    response to selenium ion    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 stimulus from selenium ion.
    GO:0033189    response to vitamin A    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 vitamin A stimulus.
    GO:0033280    response to vitamin D    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 vitamin D stimulus.
    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:0060528    secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development    The process in which a relatively unspecialized epithelial cell acquires specialized features of a secretory columnal luminar epithelial cell of the prostate.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    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.
    GO:0055012    ventricular cardiac muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a ventricular cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The ventricle is the part of the heart that pumps blood out of the organ.
    GO:0055010    ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0006766    vitamin metabolic process    The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
cellular component
    GO:0090575    RNA polymerase II transcription factor complex    A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

Chain B   (NCOA2_HUMAN | Q15596)
molecular function
    GO:0070182    DNA polymerase binding    Interacting selectively and non-covalently with a DNA polymerase.
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0001162    RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0030331    estrogen receptor binding    Interacting selectively and non-covalently with an estrogen receptor.
    GO:0035259    glucocorticoid receptor binding    Interacting selectively and non-covalently with a glucocorticoid receptor.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0030374    ligand-dependent nuclear receptor transcription coactivator activity    The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
    GO:0035257    nuclear hormone receptor binding    Interacting selectively and non-covalently with a nuclear hormone receptor, a ligand-dependent receptor found in the nucleus of the cell.
    GO:0033142    progesterone receptor binding    Interacting selectively and non-covalently with a progesterone receptor.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0042974    retinoic acid receptor binding    Interacting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily.
    GO:0046965    retinoid X receptor binding    Interacting selectively and non-covalently with a retinoid X receptor.
    GO:0046966    thyroid hormone receptor binding    Interacting selectively and non-covalently with a thyroid hormone receptor.
    GO:0030375    thyroid hormone receptor coactivator activity    The function of a transcription cofactor that activates transcription in conjunction with a thyroid hormone-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0015721    bile acid and bile salt transport    The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:1904017    cellular response to Thyroglobulin triiodothyronine    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 Thyroglobulin triiodothyronine stimulus.
    GO:0032870    cellular response to hormone stimulus    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 hormone stimulus.
    GO:0021549    cerebellum development    The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0045475    locomotor rhythm    The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045925    positive regulation of female receptivity    Any process that activates or increases the receptiveness of a female to male advances.
    GO:2000324    positive regulation of glucocorticoid receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of glucocorticoid receptor signaling pathway.
    GO:2000273    positive regulation of receptor activity    Any process that activates or increases the frequency, rate or extent of receptor activity.
    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:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0048786    presynaptic active zone    A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.
    GO:0005791    rough endoplasmic reticulum    The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOA2_HUMAN | Q155961gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iqr 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nie 4nqa 4oc7 4p6w 4p6x 4pld 4ple 4poh 4poj 4pp3 4pp5 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udc 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5i4v 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5u2d
        RXRA_HUMAN | P197931by4 1dsz 1fby 1fm6 1fm9 1g1u 1g5y 1k74 1lbd 1mv9 1mvc 1mzn 1r0n 1rdt 1rxr 1xls 1xv9 1xvp 1ynw 2acl 2nll 2p1u 2p1v 2zxz 2zy0 3dzu 3dzy 3e00 3e94 3fal 3fc6 3fug 3h0a 3kwy 3nsp 3nsq 3oap 3ozj 3pcu 3r29 3r2a 3r5m 3uvv 4cn2 4cn3 4cn5 4cn7 4j5w 4j5x 4k4j 4k6i 4m8e 4m8h 4n5g 4n8r 4nqa 4oc7 4poh 4poj 4pp3 4pp5 4rfw 4rmc 4rmd 4rme 4zo1 4zsh 5ec9 5ji0 5lyq

(-) Related Entries Specified in the PDB File

1fby SAME PROTEIN BOUND TO 9 CIS RETINOIC ACID
1lbd UNLIGANDED RECEPTOR
1mvc SAME PROTEIN BOUND TO THE SYNTHETIC AGONISTS BMS649
1xdk SAME PROTEIN BOUND TO 9 CIS RETINOIC ACID AND IN A HETERODIMERIC COMPLEX WITH RAR
2p1u
2p1v