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Asym./Biol. Unit (Jmol Viewer)

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

Title :   NUCLEAR RECEPTOR DAF-12 FROM PARASITIC NEMATODE STRONGYLOIDES STERCORALIS IN COMPLEX WITH ITS PHYSIOLOGICAL LIGAND DAFACHRONIC ACID DELTA 4

Authors :   X. E. Zhou, Z. Wang, K. Suino-Powell, D. L. Motola, A. Conneely, C. Ogata, K. K. Sharma, R. J. Auchus, S. A. Kliewer, H. E. Xu, D. J. Mangelsdorf

Date :   05 Apr 09 (Deposition) - 07 Jul 09 (Release) - 07 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Nuclear Receptor, Ligand Binding Domain, Dafachronic Acid, Src1, Nematode, Strongyloides Stercoralis, Dna-Binding, Metal-Binding, Nucleus, Receptor, Transcription, Transcription Regulation, Zinc, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Wang, X. E. Zhou, D. L. Motola, X. Gao, K. Suino-Powell, A. Conneely, C. Ogata, K. K. Sharma, R. J. Auchus, J. B. Lok, J. M. Hawdon, S. A. Kliewer, H. E. Xu, D. J. Mangelsdorf
Identification Of The Nuclear Receptor Daf-12 As A Therapeutic Target In Parasitic Nematodes.
Proc. Natl. Acad. Sci. Usa V. 106 9138 2009
PubMed-ID: 19497877 | Reference-DOI: 10.1073/PNAS.0904064106
(for further references see the PDB file header)

Molecule 1 - NUCLEAR HORMONE RECEPTOR OF THE STEROID/THYROID HORMONE RECEPTORS SUPERFAMILY
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	DAF-12
	Organism Scientific	:	STRONGYLOIDES STERCORALIS
	Organism Taxid	:	6248

Molecule 2 - SRC1
	Chains	:	B
	Engineered	:	YES
	Fragment	:	NUCLEAR RECEPTOR BINDING MOTIF 4
	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	DL4	1	Ligand/Ion	(14BETA,17ALPHA,25R)-3-OXOCHOLEST-4-EN-26-OIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:86 , MET A:559 , THR A:562 , THR A:597 , ARG A:599 , GLY A:600 , THR A:613 , VAL A:615 , MET A:625 , GLN A:637 , ALA A:728 , LEU A:731	BINDING SITE FOR RESIDUE DL4 A 100

(no "SS Bond" information available for 3GYT)

(no "Cis Peptide Bond" information available for 3GYT)

(no "SAP(SNP)/Variant" information available for 3GYT)

(no "PROSITE Motif" information available for 3GYT)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.5c	ENST00000348332	5c	ENSE00001412482	chr2:24807346-24807429	84	NCOA1_HUMAN	-	0	0	-	-
1.6b	ENST00000348332	6b	ENSE00001353786	chr2:24866835-24866991	157	NCOA1_HUMAN	-	0	0	-	-
1.7a	ENST00000348332	7a	ENSE00002170964	chr2:24881530-24881635	106	NCOA1_HUMAN	1-30	30	0	-	-
1.8	ENST00000348332	8	ENSE00001070983	chr2:24888618-24888784	167	NCOA1_HUMAN	30-86	57	0	-	-
1.9	ENST00000348332	9	ENSE00001781523	chr2:24896235-24896332	98	NCOA1_HUMAN	86-118	33	0	-	-
1.10	ENST00000348332	10	ENSE00001796214	chr2:24905820-24905997	178	NCOA1_HUMAN	119-178	60	0	-	-
1.11	ENST00000348332	11	ENSE00001070993	chr2:24914350-24914529	180	NCOA1_HUMAN	178-238	61	0	-	-
1.12	ENST00000348332	12	ENSE00001070995	chr2:24916121-24916216	96	NCOA1_HUMAN	238-270	33	0	-	-
1.13	ENST00000348332	13	ENSE00001070992	chr2:24920527-24920667	141	NCOA1_HUMAN	270-317	48	0	-	-
1.14	ENST00000348332	14	ENSE00001071000	chr2:24927955-24928102	148	NCOA1_HUMAN	317-366	50	0	-	-
1.15a	ENST00000348332	15a	ENSE00001070985	chr2:24929437-24930757	1321	NCOA1_HUMAN	366-806	441	0	-	-
1.16a	ENST00000348332	16a	ENSE00000808887	chr2:24933800-24933980	181	NCOA1_HUMAN	807-867	61	0	-	-
1.17	ENST00000348332	17	ENSE00000808888	chr2:24949458-24949575	118	NCOA1_HUMAN	867-906	40	0	-	-
1.18	ENST00000348332	18	ENSE00000808889	chr2:24951177-24951345	169	NCOA1_HUMAN	906-962	57	0	-	-
1.19	ENST00000348332	19	ENSE00000808890	chr2:24952370-24952684	315	NCOA1_HUMAN	963-1067	105	0	-	-
1.20	ENST00000348332	20	ENSE00000726392	chr2:24962301-24962402	102	NCOA1_HUMAN	1068-1101	34	0	-	-
1.21	ENST00000348332	21	ENSE00000726395	chr2:24964653-24965055	403	NCOA1_HUMAN	1102-1236	135	0	-	-
1.22	ENST00000348332	22	ENSE00000808891	chr2:24974851-24975025	175	NCOA1_HUMAN	1236-1294	59	0	-	-
1.23	ENST00000348332	23	ENSE00000726401	chr2:24980842-24981025	184	NCOA1_HUMAN	1294-1355	62	0	-	-
1.24	ENST00000348332	24	ENSE00000726404	chr2:24985556-24985645	90	NCOA1_HUMAN	1356-1385	30	0	-	-
1.26b	ENST00000348332	26b	ENSE00001797482	chr2:24991090-24993571	2482	NCOA1_HUMAN	1386-1441	56	1	B:742-751	10

Asymmetric/Biological Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:242
 aligned with Q9XZJ5_STRER | Q9XZJ5 from UniProtKB/TrEMBL  Length:753

    Alignment length:242
                                   521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751  
        Q9XZJ5_STRER    512 YTLSEKDLKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFLHFFNLLHSDVRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTLFLGAGNTTEAASLPKEFFATNY  753
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....ee.........ee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh................hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gyt A  512 YTLSEKDLKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFLHFFNLLHSDVRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTLFLGAGNTTEAASLPKEFFATNY  753
                                   521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751

Chain B from PDB  Type:PROTEIN  Length:10
 aligned with NCOA1_HUMAN | Q15788 from UniProtKB/Swiss-Prot  Length:1441

    Alignment length:10
                                  1441
         NCOA1_HUMAN   1432 KSLLQQLLTE 1441
               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 1 Exon 1.26b Transcript 1
                3gyt B  742 KSLLQQLLTE  751
                                   751

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 3GYT)

(no "CATH Domain" information available for 3GYT)

(no "Pfam Domain" information available for 3GYT)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9XZJ5_STRER | Q9XZJ5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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: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: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 B (NCOA1_HUMAN | Q15788)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001012	RNA polymerase II regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. 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:0001105	RNA polymerase II transcription coactivator activity	Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
	GO:0050681	androgen receptor binding	Interacting selectively and non-covalently with an androgen receptor.
	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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0030331	estrogen receptor binding	Interacting selectively and non-covalently with an estrogen 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:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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: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: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.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0030521	androgen receptor signaling pathway	Any series of molecular signals generated as a consequence of an androgen binding to its receptor.
	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:0021987	cerebral cortex development	The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
	GO:0044849	estrous cycle	A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur.
	GO:0021766	hippocampus development	The progression of the hippocampus over time from its initial formation until its mature state.
	GO:0043967	histone H4 acetylation	The modification of histone H4 by the addition of an acetyl group.
	GO:0021854	hypothalamus development	The progression of the hypothalamus region of the forebrain, from its initial formation to its mature state.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0060713	labyrinthine layer morphogenesis	The process in which the labyrinthine layer of the placenta is generated and organized.
	GO:0007595	lactation	The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
	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:0060179	male mating behavior	The specific behavior of a male organism that is associated with reproduction.
	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:0045925	positive regulation of female receptivity	Any process that activates or increases the receptiveness of a female to male advances.
	GO:0045666	positive regulation of neuron differentiation	Any process that activates or increases the frequency, rate or extent of neuron differentiation.
	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:0000435	positive regulation of transcription from RNA polymerase II promoter by galactose	Any process involving galactose that activates or increases the rate 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:2001141	regulation of RNA biosynthetic process	Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
	GO:2001038	regulation of cellular response to drug	Any process that modulates the frequency, rate or extent of cellular response to drug.
	GO:0002155	regulation of thyroid hormone mediated signaling pathway	Any process that modulates the frequency, rate or extent of a thyroid hormone mediated signaling pathway.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0009725	response to hormone	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 hormone stimulus.
	GO:0032570	response to progesterone	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 progesterone 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: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:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	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.

Asymmetric/Biological Unit
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	3gyt
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