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(-) Description

Title :  STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR
 
Authors :  L. Z. Mi, S. Devarakonda, J. M. Harp, Q. Han, R. Pellicciari, T. M. Willson, S. Khorasanizadeh, F. Rastinejad
Date :  20 Mar 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D,E  (1x)
Keywords :  Lbd, Bile Acid, Coactivator, Nuclear Receptor, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Z. Mi, S. Devarakonda, J. M. Harp, Q. Han, R. Pellicciari, T. M. Willson, S. Khorasanizadeh, F. Rastinejad
Structural Basis For Bile Acid Binding And Activation Of The Nuclear Receptor Fxr
Mol. Cell V. 11 1093 2003
PubMed-ID: 12718893  |  Reference-DOI: 10.1016/S1097-2765(03)00112-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BILE ACID RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN (FXR-LBD)
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: FARNESOID X-ACTIVATED RECEPTOR, FARNESOL RECEPTOR HRR-1, RETINOID X RECEPTOR-INTERACTING PROTEIN 14, RXR- INTERACTING PROTEIN 14
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: C, D, E
    Engineered: YES
    Fragment: RESIDUES (741-752)
    Other Details: THE COACTIVATOR PEPTIDE WAS SYNTHESIZED. THE SEQUENCE OF THE GRIP IS NATURALLY FOUND IN RATTUS NORVEGICUS (NORWAY RAT).
    Synonym: NCOA-2, TRANSCRIPTION INTERMEDIARY FACTOR 2, GLUCOCORTICOID RECEPTOR-INTERACTING PROTEIN 1, GRIP-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A C  
Biological Unit 2 (1x):  B DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CHC2Ligand/Ion6-ETHYL-CHENODEOXYCHOLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CHC1Ligand/Ion6-ETHYL-CHENODEOXYCHOLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CHC1Ligand/Ion6-ETHYL-CHENODEOXYCHOLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:262 , LEU B:284 , MET B:287 , ALA B:288 , HIS B:291 , MET B:325 , PHE B:326 , ARG B:328 , SER B:329 , PHE B:333 , ILE B:349 , TYR B:358 , PHE B:363 , TYR B:366 , HIS B:444BINDING SITE FOR RESIDUE CHC B 201
2AC2SOFTWAREMET A:262 , MET A:325 , PHE A:326 , ARG A:328 , SER A:329 , ILE A:349 , TYR A:358 , MET A:362 , TYR A:366 , HIS A:444 , TRP A:466BINDING SITE FOR RESIDUE CHC A 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:423 -Pro A:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000099101ENSRNOE00000353369chr7:26307061-26306959103NR1H4_RAT-00--
1.2ENSRNOT000000099102ENSRNOE00000069662chr7:26276740-26276606135NR1H4_RAT1-23230--
1.4ENSRNOT000000099104ENSRNOE00000066613chr7:26258318-26257950369NR1H4_RAT23-1461240--
1.5aENSRNOT000000099105aENSRNOE00000336037chr7:26240305-26240165141NR1H4_RAT146-193480--
1.6ENSRNOT000000099106ENSRNOE00000066952chr7:26237700-26237567134NR1H4_RAT193-237450--
1.7ENSRNOT000000099107ENSRNOE00000067172chr7:26235927-2623582999NR1H4_RAT238-270332A:240-270
B:240-270		31
31
1.8ENSRNOT000000099108ENSRNOE00000067330chr7:26235495-26235396100NR1H4_RAT271-304342A:271-304
B:271-304		34
34
1.9ENSRNOT000000099109ENSRNOE00000067481chr7:26230774-26230628147NR1H4_RAT304-353502A:304-353
B:304-353		50
50
1.10ENSRNOT0000000991010ENSRNOE00000067646chr7:26191941-26191828114NR1H4_RAT353-391392A:353-391
B:353-391		39
39
1.11ENSRNOT0000000991011ENSRNOE00000342572chr7:26190485-26189759727NR1H4_RAT391-469792A:391-468
B:391-468		78
78

(-) 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:229
 aligned with NR1H4_RAT | Q62735 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:229
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
            NR1H4_RAT   240 TELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
               SCOP domains d1osva_ A: Bile acid receptor FXR                                                                                                                                                                                                     SCOP domains
               CATH domains 1osvA00 A:240-468 Retinoid X Receptor                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:240-270       Exon 1.8  PDB: A:271-304          ------------------------------------------------Exon 1.10  PDB: A:353-391              ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.9  PDB: A:304-353 UniProt: 304-353         -------------------------------------Exon 1.11  PDB: A:391-468 UniProt: 391-469 [INCOMPLETE]                        Transcript 1 (2)
                 1osv A 240 AELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with NR1H4_RAT | Q62735 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:229
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
            NR1H4_RAT   240 TELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
               SCOP domains d1osvb_ B: Bile acid receptor FXR                                                                                                                                                                                                     SCOP domains
               CATH domains 1osvB00 B:240-468 Retinoid X Receptor                                                                                                                                                                                                 CATH domains
           Pfam domains (1) --Hormone_recep-1osvB01 B:242-461                                                                                                                                                                                             ------- Pfam domains (1)
           Pfam domains (2) --Hormone_recep-1osvB02 B:242-461                                                                                                                                                                                             ------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: B:240-270       Exon 1.8  PDB: B:271-304          ------------------------------------------------Exon 1.10  PDB: B:353-391              ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.9  PDB: B:304-353 UniProt: 304-353         -------------------------------------Exon 1.11  PDB: B:391-468 UniProt: 391-469 [INCOMPLETE]                        Transcript 1 (2)
                 1osv B 240 AELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         


Chain C from PDB  Type:PROTEIN  Length:12
 aligned with NCOA2_MOUSE | Q61026 from UniProtKB/Swiss-Prot  Length:1462

    Alignment length:12
                                   750  
          NCOA2_MOUSE   741 ENALLRYLLDKD 752
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1osv C   1 ENALLRYLLDKD  12
                                    10  


Chain D from PDB  Type:PROTEIN  Length:12
 aligned with NCOA2_MOUSE | Q61026 from UniProtKB/Swiss-Prot  Length:1462

    Alignment length:12
                                   750  
          NCOA2_MOUSE   741 ENALLRYLLDKD 752
               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
                 1osv D   1 ENALLRYLLDKD  12
                                    10  


Chain E from PDB  Type:PROTEIN  Length:12
 aligned with NCOA2_MOUSE | Q61026 from UniProtKB/Swiss-Prot  Length:1462

    Alignment length:12
                                   750  
          NCOA2_MOUSE   741 ENALLRYLLDKD 752
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1osv E   1 ENALLRYLLDKD  12
                                    10
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Hormone_recep] (290)

(-) Gene Ontology  (76, 83)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NR1H4_RAT | Q62735)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0038181    bile acid receptor activity    Combining with a bile acid and transmitting the signal to initiate a change in cell activity. A bile acid is any member of a group of steroid carboxylic acids occurring in bile.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0004887    thyroid hormone receptor activity    Combining with thyroid hormone 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: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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific 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 (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008206    bile acid metabolic process    The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
    GO:0038183    bile acid signaling pathway    A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    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: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:0006109    regulation of carbohydrate metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009749    response to glucose    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 glucose stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.

Chain C,D,E   (NCOA2_MOUSE | Q61026)
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: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)

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        NCOA2_MOUSE | Q61026: 1l2i 1wm0 2q6j 2qa6 2qa8 2qab 2qgt 2qgw 2qh6 2qpy 2qr9 2qse 2qxm 2qzo 3mne 3mno 3mnp
        NR1H4_RAT | Q62735: 1ot7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1OSV)