2ZMI - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF RAT VITAMIN D RECEPTOR BOUND TO ADAMANTYL VITAMIN D ANALOGS: STRUCTURAL BASIS FOR VITAMIN D RECEPTOR ANTAGONISM AND/OR PARTIAL AGONISM

Authors :   M. Nakabayashi, S. Yamada, T. Tanaka, M. Igarashi, N. Yoshimoto, T. Ikura, N. Ito, M. Makishima, H. Tokiwa, H. F. Deluca, M. Shimizu

Date :   19 Apr 08 (Deposition) - 02 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Nuclear Receptor-Antagonist Complex, Dna-Binding, Metal- Binding, Nucleus, Phosphoprotein, Receptor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nakabayashi, S. Yamada, N. Yoshimoto, T. Tanaka, M. Igarashi, T. Ikura, N. Ito, M. Makishima, H. Tokiwa, H. F. Deluca, M. Shimizu
Crystal Structures Of Rat Vitamin D Receptor Bound To Adamantyl Vitamin D Analogs: Structural Basis For Vitamin D Receptor Antagonism And Partial Agonism
J. Med. Chem. V. 51 5320 2008
PubMed-ID: 18710208 | Reference-DOI: 10.1021/JM8004477
(for further references see the PDB file header)

Molecule 1 - VITAMIN D3 RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-14B
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN, UNP RESIDUES 116-423
	Gene	:	VDR, NR1I1
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1

Molecule 2 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1
	Chains	:	C
	Engineered	:	YES
	Fragment	:	DRIP 205 NR2 BOX PEPTIDE, UNP RESIDUES 624-636
	Other Details	:	SYNTHETIC PEPTIDE
	Synonym	:	MEDIATOR COMPLEX SUBUNIT 1, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	FMT	1	Ligand/Ion	FORMIC ACID
3	TT2	1	Ligand/Ion	(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-5-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENT-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:143 , LEU A:223 , ALA A:227 , SER A:233 , MET A:268 , ARG A:270 , SER A:271 , SER A:274 , TRP A:282 , CYS A:284 , ALA A:299 , HIS A:301 , HIS A:393 , LEU A:410	BINDING SITE FOR RESIDUE TT2 A 1
2	AC2	SOFTWARE	PRO A:412 , LEU A:415 , ASN A:420 , HOH A:496	BINDING SITE FOR RESIDUE EDO A 424
3	AC3	SOFTWARE	SER A:356 , HOH A:439	BINDING SITE FOR RESIDUE FMT A 425

(no "SS Bond" information available for 2ZMI)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:369	-	Pro A:370

(no "SAP(SNP)/Variant" information available for 2ZMI)

(no "PROSITE Motif" information available for 2ZMI)

(no "Exon" information available for 2ZMI)

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:242
 aligned with VDR_RAT | P13053 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:300
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
              VDR_RAT   121 RPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSYSPRPTLSFSGNSSSSSSDLYTTSLDMMEPSGFSNLDLNGEDSDDPSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN 420
               SCOP domains d2zmia_ A: Vitamin D nuclear receptor                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2zmiA00 A:121-420 Retinoid X Receptor                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------Hormone_recep-2zmiA01 A:218-414                                                                                                                                                                      ------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh...hhhhhhh......----------------------------------------------------------....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee......eehhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zmi A 121 RPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRM----------------------------------------------------------SPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN 420
                                   130       140       150        |-         -         -         -         -         -       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
                                                                159                                                        218

Chain C from PDB  Type:PROTEIN  Length:11
 aligned with MED1_XENTR | A1L0Z0 from UniProtKB/Swiss-Prot  Length:1573

    Alignment length:11
                                   633 
           MED1_XENTR   624 KNHPMLMNLLK 634
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 2zmi C 625 KNHPMLMNLLK 635
                                   634

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)

Norway rat (Rattus norvegicus) [TaxId: 10116] (15)

d2zmia_

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)

Rat (Rattus norvegicus) (10)

2zmiA00

A:121-420

Asymmetric/Biological Unit

Clans(

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Families(

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Organisms( (-)

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

Family: Hormone_recep (290)

Rattus norvegicus (Rat) (22)

Hormone_recep-2zmiA01

A:218-414

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VDR_RAT | P13053)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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: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:0005499	vitamin D binding	Interacting selectively and non-covalently with vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0071305	cellular response to vitamin D	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 vitamin D stimulus.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0051924	regulation of calcium ion transport	Any process that modulates the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0051592	response to calcium ion	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 calcium ion stimulus.
	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: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.
	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:0030315	T-tubule	Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
	GO:0005901	caveola	A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0001651	dense fibrillar component	A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins.
	GO:0000791	euchromatin	A dispersed and relatively uncompacted form of chromatin.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Chain C (MED1_XENTR | A1L0Z0)

molecular function
	GO:0001104	RNA polymerase II transcription cofactor 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 modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.
	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:0046966	thyroid hormone receptor binding	Interacting selectively and non-covalently with a thyroid hormone receptor.
	GO:0030375	thyroid hormone receptor coactivator activity	The function of a transcription cofactor that activates transcription in conjunction with a thyroid hormone-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
	GO:0042809	vitamin D receptor binding	Interacting selectively and non-covalently with the vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes.
biological process
	GO:0097067	cellular response to thyroid hormone stimulus	A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
	GO:2000273	positive regulation of receptor activity	Any process that activates or increases the frequency, rate or extent of receptor activity.
	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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016592	mediator complex	A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
	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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	Cis Peptide Bonds
		Pro A:369 - Pro A:370	[ RasMol ]

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	2zmi
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	VDR_RAT \| P13053
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2zmh	THE SAME PROTEIN COMPLEXED WITH ADNY
2zmj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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