1YP0 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF THE STEROIDOGENIC FACTOR-1 LIGAND BINDING DOMAIN BOUND TO PHOSPHOLIPID AND A SHP PEPTIDE MOTIF

Authors :   Y. Li, M. Choi, G. Cavey, J. Daugherty, K. Suino, A. Kovach, N. Bingham, S. Kliewer, H. Xu

Date :   28 Jan 05 (Deposition) - 19 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ligand Dependent Nuclear Receptor, Steroidogenic Factor-1, Nr5A1, Helical Sandwich Fold, Lbd Fold, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Li, M. Choi, G. Cavey, J. Daugherty, K. Suino, A. Kovach, N. Bingham, S. Kliewer, H. Xu
Crystallographic Identification And Functional Characterization Of Phospholipids As Ligands For The Orphan Nuclear Receptor Steroidogenic Factor-1.
Mol. Cell V. 17 491 2005
PubMed-ID: 15721253 | Reference-DOI: 10.1016/J.MOLCEL.2005.02.002
(for further references see the PDB file header)

Molecule 1 - NUCLEAR RECEPTOR SUBFAMILY 5, GROUP A, MEMBER 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	T7 PROMOTER
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - NUCLEAR RECEPTOR SUBFAMILY 0, GROUP B, MEMBER 2
	Chains	:	B
	Engineered	:	YES
	Fragment	:	SHP LXXLL
	Other Details	:	PEPTIDE SYNTHESIS, THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN RATTUS NORVEGICUS (NORWAY RAT)
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PEF	1	Ligand/Ion	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:22 , PHE A:263 , LEU A:266 , ARG A:283 , LEU A:307 , HIS A:311 , GLN A:340 , GLY A:342 , LEU A:345 , ALA A:352 , TYR A:437 , LYS A:441	BINDING SITE FOR RESIDUE PEF A 201

(no "SS Bond" information available for 1YP0)

(no "Cis Peptide Bond" information available for 1YP0)

(no "SAP(SNP)/Variant" information available for 1YP0)

(no "PROSITE Motif" information available for 1YP0)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000009683	1	ENSRNOE00000066760	chr5:151528000-151527426	575	NR0B2_RAT	1-181	181	1	B:17-28	12
1.2	ENSRNOT00000009683	2	ENSRNOE00000067358	chr5:151525220-151524685	536	NR0B2_RAT	181-260	80	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:239
 aligned with STF1_MOUSE | P33242 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:239
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
           STF1_MOUSE   223 NVPELILQLLQLEPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAKQ 461
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yp0A00 A:223-461 Retinoid X Receptor                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------Hormone_recep-1yp0A01 A:251-456                                                                                                                                                                               ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yp0 A 223 NVPELILQLLQLEPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAKQ 461
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452

Chain B from PDB  Type:PROTEIN  Length:12
 aligned with NR0B2_RAT | P97947 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:12
                                    26  
            NR0B2_RAT    17 HPTILYTLLSPG  28
               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 1 Exon 1.1     Transcript 1
                 1yp0 B  17 HPTILYTLLSPG  28
                                    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 '\|'

(no "SCOP Domain" information available for 1YP0)

Asymmetric/Biological 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)

House mouse (Mus musculus) (11)

1yp0A00

A:223-461

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Hormone_recep (290)

Mus musculus (Mouse) (10)

Hormone_recep-1yp0A01

A:251-456

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (STF1_MOUSE | P33242)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030325	adrenal gland development	The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0008585	female gonad development	The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
	GO:0042445	hormone metabolic process	The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
	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:0001553	luteinization	The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation.
	GO:0051457	maintenance of protein location in nucleus	Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus.
	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:0010259	multicellular organism aging	An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700).
	GO:2000195	negative regulation of female gonad development	Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.
	GO:2000020	positive regulation of male gonad development	Any process that activates or increases the frequency, rate or extent of male gonad development.
	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: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:0022414	reproductive process	A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
	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: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: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 B (NR0B2_RAT | P97947)

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: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: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: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: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.

Asymmetric/Biological Unit
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	STF1_MOUSE \| P33242
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	NR0B2_RAT \| P97947	:	1zgy 1zh7
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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

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