1S19 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF VDR LIGAND BINDING DOMAIN COMPLEXED TO CALCIPOTRIOL.

Authors :   G. Tocchini-Valentini, N. Rochel, J. M. Wurtz, D. Moras

Date :   06 Jan 04 (Deposition) - 13 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Nuclear Receptor, Transcription Regulation, Alpha-Helical Sandwich, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Tocchini-Valentini, N. Rochel, J. M. Wurtz, D. Moras
Crystal Structures Of The Vitamin D Nuclear Receptor Liganded With The Vitamin D Side Chain Analogues Calcipotriol And Seocalcitol, Receptor Agonists Of Clinical Importance. Insights Into A Structural Basis For The Switching Of Calcipotriol To A Receptor Antagonist By Further Side Chain Modification.
J. Med. Chem. V. 47 1956 2004
PubMed-ID: 15055995 | Reference-DOI: 10.1021/JM0310582
(for further references see the PDB file header)

Molecule 1 - VITAMIN D3 RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	VDR LIGAND BINDING DOMAIN
	Gene	:	VDR, NR1I1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MC9	1	Ligand/Ion	CALCIPOTRIOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:143 , LEU A:227 , LEU A:233 , VAL A:234 , SER A:237 , ARG A:274 , SER A:275 , SER A:278 , TRP A:286 , CYS A:288 , HIS A:305 , LEU A:309 , HIS A:397	BINDING SITE FOR RESIDUE MC9 A 500

(no "SS Bond" information available for 1S19)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:373	-	Pro A:374

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029309	L	230	V	VDR_HUMAN	Polymorphism	11574090	A	L	230	V
2	UniProt	VAR_004664	R	274	L	VDR_HUMAN	Disease (VDDR2A)	121909796	A	R	274	L
3	UniProt	VAR_004665	H	305	Q	VDR_HUMAN	Disease (VDDR2A)	121909798	A	H	305	Q
4	UniProt	VAR_004666	I	314	S	VDR_HUMAN	Disease (VDDR2A)	121909799	A	I	314	S
5	UniProt	VAR_029310	T	362	I	VDR_HUMAN	Polymorphism	11574115	A	T	362	I
6	UniProt	VAR_004667	R	391	C	VDR_HUMAN	Disease (VDDR2A)	121909800	A	R	391	C

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

(no "PROSITE Motif" information available for 1S19)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000395324	1	ENSE00001485612	chr12:48298814-48298738	77	VDR_HUMAN	-	0	0	-	-
1.3	ENST00000395324	3	ENSE00001354497	chr12:48276557-48276477	81	VDR_HUMAN	-	0	0	-	-
1.4	ENST00000395324	4	ENSE00000888048	chr12:48272898-48272751	148	VDR_HUMAN	1-49	49	0	-	-
1.5	ENST00000395324	5	ENSE00000738168	chr12:48258960-48258830	131	VDR_HUMAN	49-93	45	0	-	-
1.6	ENST00000395324	6	ENSE00000738167	chr12:48251471-48251287	185	VDR_HUMAN	93-154	62	1	A:120-154	35
1.7	ENST00000395324	7	ENSE00000738166	chr12:48251032-48250912	121	VDR_HUMAN	155-195	41	1	A:155-164	10
1.8	ENST00000395324	8	ENSE00000738165	chr12:48249584-48249413	172	VDR_HUMAN	195-252	58	1	A:216-252	37
1.9	ENST00000395324	9	ENSE00000738164	chr12:48240591-48240440	152	VDR_HUMAN	252-303	52	1	A:252-303	52
1.10	ENST00000395324	10	ENSE00000738163	chr12:48240234-48240118	117	VDR_HUMAN	303-342	40	1	A:303-342	40
1.11	ENST00000395324	11	ENSE00001419012	chr12:48238788-48235322	3467	VDR_HUMAN	342-427	86	1	A:342-423	82

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:253
 aligned with VDR_HUMAN | P11473 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:304
                                   129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419    
            VDR_HUMAN   120 LRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSHPSRPNSRHTPSFSGDSSSSCSDHCITSSDMMDSSSFSNLDLSEEDSDDPSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
               SCOP domains d1s19a_ A: Vitamin D nuclear receptor                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1s19A00 A:120-423 Retinoid X Receptor                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------Hormone_recep-1s19A01 A:216-418                                                                                                                                                                            ----- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....hhhhh...........---------------------------------------------------hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee..hhh.eehhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------V-------------------------------------------L------------------------------Q--------S-----------------------------------------------I----------------------------C-------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:120-154           Exon 1.7  PDB: A:155-164 UniProt: 155-195-----------------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:303-342               --------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------Exon 1.8  PDB: A:216-252 UniProt: 195-252 [INCOMPLETE]    -----------------------------------------------------------------------------------------Exon 1.11  PDB: A:342-423 UniProt: 342-427 [INCOMPLETE]                            Transcript 1 (2)
           Transcript 1 (3) ------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:252-303 UniProt: 252-303           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (3)
                 1s19 A 120 LRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGG---------------------------------------------------SVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
                                   129       139       149       159    |    -         -         -         -         -      |219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419    
                                                                      164                                                 216

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Vitamin D nuclear receptor (37)

Human (Homo sapiens) [TaxId: 9606] (22)

d1s19a_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Retinoid X Receptor (409)

Homologous Superfamily: Retinoid X Receptor (409)

Human (Homo sapiens) (337)

1s19A00

A:120-423

Asymmetric/Biological Unit

Clans(

)

Families(

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Organisms( (-)

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

Family: Hormone_recep (290)

Homo sapiens (Human) (244)

Hormone_recep-1s19A01

A:216-418

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VDR_HUMAN | P11473)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:1902098	calcitriol binding	Interacting selectively and non-covalently with calcitriol. Calcitriol (1,25-dihydroxycholecalciferol) is the hormonally active form of vitamin D3.
	GO:0008434	calcitriol receptor activity	Combining with calcitriol, the hormonally active form of vitamin D3, 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:1902121	lithocholic acid binding	Interacting selectively and non-covalently with lithocholic acid.
	GO:0038186	lithocholic acid receptor activity	Combining with lithocholic acid and transmitting the signal to initiate a change in cell activity.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046965	retinoid X receptor binding	Interacting selectively and non-covalently with a retinoid X receptor.
	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: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:0070644	vitamin D response element binding	Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0009887	animal organ morphogenesis	Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
	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:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0006874	cellular calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
	GO:0046697	decidualization	The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation. This process involves the proliferation and differentiation of the fibroblast-like endometrial stromal cells into large, polyploid decidual cells that eventually form the maternal component of the placenta.
	GO:0050892	intestinal absorption	Any process in which nutrients are taken up from the contents of the intestine.
	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:0060745	mammary gland branching involved in pregnancy	The process in which the branching structure of the mammary gland duct is generated and organized as a part of pregnancy.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010839	negative regulation of keratinocyte proliferation	Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population.
	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:0060058	positive regulation of apoptotic process involved in mammary gland involution	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process of mammary epithelial cells during mammary gland involution.
	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:0045618	positive regulation of keratinocyte differentiation	Any process that activates or increases the frequency, rate or extent of keratinocyte 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:0010980	positive regulation of vitamin D 24-hydroxylase activity	Any process that increases the rate, frequency or extent of vitamin D 24-hydroxylase activity. Vitamin D 24-hydroxylase activity catalyzes the hydroxylation of C-24 of any form of vitamin D.
	GO:0060558	regulation of calcidiol 1-monooxygenase activity	Any process that modulates the rate, frequency or extent of calcidiol 1-monooxygenase activity. Calcidiol 1-monooxygenase activity is catalysis of the reaction: calcidiol + NADPH + H+ + O2 = calcitriol + NADP+ + H2O.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	GO:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0070561	vitamin D receptor signaling pathway	The series of molecular signals generated as a consequence of a vitamin D receptor binding to one of its physiological ligands.
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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

Asymmetric/Biological Unit
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	1s19
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1db1	VDR LBD COMPLEXED TO VATIMIN D
1ie8	VDR LBD COMPLEXED TO KH1060
1ie9	VDR LBD COMPLEXED TO MC2100
1s0z	VDR LBD COMPEXED TO SEOCALCITOL

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Ligands, Modified Residues, Ions (1, 1)

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