1YUC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   HUMAN NUCLEAR RECEPTOR LIVER RECEPTOR HOMOLOGUE-1, LRH-1, BOUND TO PHOSPHOLIPID AND A FRAGMENT OF HUMAN SHP

Authors :   E. A. Ortlund, L. Yoonkwang, I. H. Solomon, J. M. Hager, R. Safi, Y. Choi, A. Tripathy, C. R. H. Raetz, D. P. Mcdonnell, D. D. Moore, M. R. Redinbo

Date :   13 Feb 05 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4: A,B,C,D  (1x)

Keywords :   Liver Receptor Homologue 1; Nuclear Receptor Ligand Binding Domain; Lrh-1; Phospholipid; Shp; Small Heterodimer Partner, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. A. Ortlund, Y. Lee, I. H. Solomon, J. M. Hager, R. Safi, Y. Choi, Z. Guan, A. Tripathy, C. R. H. Raetz, D. P. Mcdonnell, D. D. Moore, M. R. Redinbo
Modulation Of Human Nuclear Receptor Lrh-1 Activity By Phospholipids And Shp
Nat. Struct. Mol. Biol. V. 12 357 2005
PubMed-ID: 15723037 | Reference-DOI: 10.1038/NSMB910

Molecule 1 - ORPHAN NUCLEAR RECEPTOR NR5A2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALCH10T
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	NR5A2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALPHA-1-FETOPROTEIN TRANSCRIPTION FACTOR

Molecule 2 - NUCLEAR RECEPTOR 0B2
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	NR BOX1
	Other Details	:	SEQUENCE OCCURS NATUARLLY IN HOMO SAPIENS
	Synonym	:	ORPHAN NUCLEAR RECEPTOR SHP; SMALL HETERODIMER PARTNER
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 4 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EPH	2	Ligand/Ion	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	EPH	1	Ligand/Ion	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	EPH	1	Ligand/Ion	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	EPH	1	Ligand/Ion	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	EPH	2	Ligand/Ion	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2	GOL	3	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:494 , GLY A:497 , HOH B:41	BINDING SITE FOR RESIDUE GOL A 5001
2	AC2	SOFTWARE	GLN A:498 , ARG A:502 , HOH B:212 , LEU B:482 , ASP B:483	BINDING SITE FOR RESIDUE GOL B 5002
3	AC3	SOFTWARE	HOH A:142 , HOH B:8 , HOH B:34 , GLU B:384 , SER B:458 , ASP B:460 , LEU B:503	BINDING SITE FOR RESIDUE GOL B 5003

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

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

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

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

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000254227	1	ENSE00000761012	chr1:27240457-27239900	558	NR0B2_HUMAN	1-178	178	2	C:15-28 D:17-27	14 11
1.2	ENST00000254227	2	ENSE00001065528	chr1:27238577-27237980	598	NR0B2_HUMAN	178-257	80	0	-	-

2.1a	ENST00000367362	1a	ENSE00001869866	chr1:199996730-199997039	310	NR5A2_HUMAN	1-22	22	0	-	-
2.4b	ENST00000367362	4b	ENSE00001624402	chr1:200008786-200008923	138	NR5A2_HUMAN	22-68	47	0	-	-
2.5a	ENST00000367362	5a	ENSE00001705336	chr1:200012902-200013020	119	NR5A2_HUMAN	68-107	40	0	-	-
2.6	ENST00000367362	6	ENSE00001742097	chr1:200014571-200014712	142	NR5A2_HUMAN	108-155	48	0	-	-
2.7	ENST00000367362	7	ENSE00001616774	chr1:200017300-200017946	647	NR5A2_HUMAN	155-370	216	2	A:299-370 B:300-370	72 71
2.9	ENST00000367362	9	ENSE00001680332	chr1:200080330-200080449	120	NR5A2_HUMAN	371-410	40	2	A:371-410 B:371-410	40 40
2.10	ENST00000367362	10	ENSE00001632410	chr1:200089936-200090083	148	NR5A2_HUMAN	411-460	50	2	A:411-460 B:411-460	50 50
2.11b	ENST00000367362	11b	ENSE00001420464	chr1:200143091-200146552	3462	NR5A2_HUMAN	460-541	82	2	A:460-538 B:460-539	79 80

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:240
 aligned with NR5A2_HUMAN | O00482 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:240
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538
          NR5A2_HUMAN   299 ASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 538
               SCOP domains d1yuca_ A: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 1yucA00 A:299-538 Retinoid X Receptor                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.7  PDB: A:299-370 UniProt: 155-370 [INCOMPLETE]                  Exon 2.9  PDB: A:371-410                Exon 2.10  PDB: A:411-460 UniProt: 411-460        ------------------------------------------------------------------------------ Transcript 2 (1)
           Transcript 2 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.11b  PDB: A:460-538 UniProt: 460-541 [INCOMPLETE]                        Transcript 2 (2)
                 1yuc A 299 ASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 538
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538

Chain B from PDB  Type:PROTEIN  Length:240
 aligned with NR5A2_HUMAN | O00482 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:240
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539
          NR5A2_HUMAN   300 SIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK 539
               SCOP domains d1yucb_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 1yucB00 B:300-539 Retinoid X Receptor                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ------------------------Hormone_recep-1yucB01 B:324-535                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) ------------------------Hormone_recep-1yucB02 B:324-535                                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.7  PDB: B:300-370 UniProt: 155-370 [INCOMPLETE]                 Exon 2.9  PDB: B:371-410                Exon 2.10  PDB: B:411-460 UniProt: 411-460        ------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.11b  PDB: B:460-539 UniProt: 460-541 [INCOMPLETE]                         Transcript 2 (2)
                 1yuc B 300 SIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK 539
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539

Chain C from PDB  Type:PROTEIN  Length:14
 aligned with NR0B2_HUMAN | Q15466 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:14
                                    24    
          NR0B2_HUMAN    15 ASRPAILYALLSSS  28
               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 1 Exon 1.1       Transcript 1
                 1yuc C  15 ASRPAILYALLSSS  28
                                    24

Chain D from PDB  Type:PROTEIN  Length:11
 aligned with NR0B2_HUMAN | Q15466 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:11
                                    26 
          NR0B2_HUMAN    17 RPAILYALLSS  27
               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 1 Exon 1.1    Transcript 1
                 1yuc D  17 RPAILYALLSS  27
                                    26

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Nuclear receptor ligand-binding domain (609)

Superfamily: Nuclear receptor ligand-binding domain (609)

Family: Nuclear receptor ligand-binding domain (598)

Protein domain: automated matches (140)

Human (Homo sapiens) [TaxId: 9606] (122)

1a	d1yuca_	A:
1b	d1yucb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Retinoid X Receptor (409)

Homologous Superfamily: Retinoid X Receptor (409)

Human (Homo sapiens) (337)

1a	1yucA00	A:299-538
1b	1yucB00	B:300-539

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Hormone_recep (290)

Homo sapiens (Human) (244)

1a	Hormone_recep-1yucB01	B:324-535
1b	Hormone_recep-1yucB02	B:324-535

Asymmetric Unit(hide GO term definitions)

Chain A,B (NR5A2_HUMAN | O00482)

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:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
	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: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:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	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: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:0003705	transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP 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: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:0000976	transcription 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 transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
	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:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	GO:0009790	embryo development	The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0042592	homeostatic process	Any biological process involved in the maintenance of an internal steady state.
	GO:0009755	hormone-mediated signaling pathway	A series of molecular signals mediated by the detection of a hormone.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0061113	pancreas morphogenesis	Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045070	positive regulation of viral genome replication	Any process that activates or increases the frequency, rate or extent of viral genome replication.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	GO:0009888	tissue development	The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
	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: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:0090575	RNA polymerase II transcription factor complex	A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain C,D (NR0B2_HUMAN | Q15466)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042975	peroxisome proliferator activated receptor binding	Interacting selectively and non-covalently with any of the peroxisome proliferator activated receptors, alpha, beta or gamma.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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: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:0046966	thyroid hormone receptor binding	Interacting selectively and non-covalently with a thyroid hormone receptor.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive 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:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	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:0010629	negative regulation of gene expression	Any process that decreases 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:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	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: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:0032024	positive regulation of insulin secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

Description

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Ligands, Modified Residues, Ions (2, 5)

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