3K6P - JenaLib

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Title :   ESTROGEN RELATED RECEPTOR ALPHA IN COMPLEX WITH AN ETHER BASED LIGAND

Authors :   M. C. Abad, R. J. Patch

Date :   09 Oct 09 (Deposition) - 20 Oct 10 (Release) - 20 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Estrogen Related Receptor Alpha, Dna-Binding, Isopeptide Bond, Metal- Binding, Nucleus, Phosphoprotein, Receptor, Transcription, Transcription Regulation, Zinc-Finger, Hormone Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Patch, L. L. Searle, A. J. Kim, D. De, X. Zhu, H. B. Askari, J. C. O'Neill, M. C. Abad, D. Rentzeperis, J. G. Geisler
Development Of Diaryl Ether Based Ligands For Estrogen Related Receptor Alpha As Potential Anti-Diabetic Agents.
To Be Published
PubMed: search

Molecule 1 - STEROID HORMONE RECEPTOR ERR1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	T7 PET VECTOR
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	ERR1, ESRL1, ESRRA, NR3B1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ESTROGEN-RELATED RECEPTOR, ALPHA, ERR-ALPHA, ESTROGEN RECEPTOR-LIKE 1, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP B MEMBER 1

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	5FB	1	Ligand/Ion	4-(4-{[(5R)-2,4-DIOXO-1,3-THIAZOLIDIN-5-YL]METHYL}-2-METHOXYPHENOXY)-3-(TRIFLUOROMETHYL)BENZONITRILE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	5FB	1	Ligand/Ion	4-(4-{[(5R)-2,4-DIOXO-1,3-THIAZOLIDIN-5-YL]METHYL}-2-METHOXYPHENOXY)-3-(TRIFLUOROMETHYL)BENZONITRILE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	5FB	2	Ligand/Ion	4-(4-{[(5R)-2,4-DIOXO-1,3-THIAZOLIDIN-5-YL]METHYL}-2-METHOXYPHENOXY)-3-(TRIFLUOROMETHYL)BENZONITRILE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:28 , HOH A:61 , HIS A:280 , LEU A:282 , GLU A:283 , VAL A:284 , LEU A:324 , CYS A:325 , PHE A:328 , GLU A:331 , VAL A:369 , ARG A:372 , PHE A:382 , ALA A:396 , LEU A:398 , VAL A:491 , PHE A:495 , MET A:506	BINDING SITE FOR RESIDUE 5FB A 1

(no "SS Bond" information available for 3K6P)

(no "Cis Peptide Bond" information available for 3K6P)

(no "SAP(SNP)/Variant" information available for 3K6P)

(no "PROSITE Motif" information available for 3K6P)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000000442	1b	ENSE00001884684	chr11:64073050-64073208	159	ERR1_HUMAN	-	0	0	-	-
1.3a	ENST00000000442	3a	ENSE00001195360	chr11:64074640-64074976	337	ERR1_HUMAN	1-109	109	0	-	-
1.4b	ENST00000000442	4b	ENSE00001195352	chr11:64081423-64081539	117	ERR1_HUMAN	109-148	40	0	-	-
1.5	ENST00000000442	5	ENSE00001195345	chr11:64081711-64081839	129	ERR1_HUMAN	148-191	44	1	A:280-288 (gaps)	12
1.6a	ENST00000000442	6a	ENSE00001195335	chr11:64082213-64082383	171	ERR1_HUMAN	191-248	58	1	A:289-344 (gaps)	56
1.7	ENST00000000442	7	ENSE00000727249	chr11:64082473-64082742	270	ERR1_HUMAN	248-338	91	1	A:344-434	91
1.8b	ENST00000000442	8b	ENSE00001271942	chr11:64083179-64084210	1032	ERR1_HUMAN	338-423	86	1	A:434-518 (gaps)	85

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:226
 aligned with ERR1_HUMAN | P11474 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:260
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422
           ERR1_HUMAN   163 RRPEVDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMM 422
               SCOP domains d3k6p   a_ A                  : automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----   ----                  ---------------------       --Hormone_recep-3k6pA01 A:319-510                                                                                                                                                                 -------- Pfam domains
         Sec.struct. author ..hhh---hhh.------------------.hhhhhhhhhhhh........-------..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eeehhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.----....-hhhhhhhhhhhhhhhhhhhhhhhhhh.-.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5 UniProt: 148-191    --------------------------------------------------------Exon 1.7  PDB: A:344-434 UniProt: 248-338                                                  ------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.6a  PDB: A:289-344 (gaps) UniProt: 191-248         -----------------------------------------------------------------------------------------Exon 1.8b  PDB: A:434-518 (gaps) UniProt: 338-423 [INCOMPLETE]                        Transcript 1 (2)
                 3k6p A 280 HHLEV---LFQG------------------PVNALVSHLLVVEPEKLYAMP-------HLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGR----GGAE-RRAGRLLLTLPLLRQTAGKVLAHFYGV-LEGKVPMHKLFLEMLEAMM 518
                                |  286 |       -         -|      298       308|      318       328       338       348       358       368       378       388       398       408       418       428       438       448       458   |   468 | |   478       488       498 |     508       518
                              284 285  |                289                 309     317                                                                                                                                              462  467  | |                       498 |                  
                                     288                                                                                                                                                                                                     470 |                         500                  
                                                                                                                                                                                                                                               472

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)

d3k6pa_

(no "CATH Domain" information available for 3K6P)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Hormone_recep (290)

Homo sapiens (Human) (244)

Hormone_recep-3k6pA01

A:319-510

Asymmetric Unit(hide GO term definitions)

Chain A (ERR1_HUMAN | P11474)

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: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: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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	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:0005496	steroid binding	Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
	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: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:0001078	transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0007005	mitochondrion organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
	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:1900078	positive regulation of cellular response to insulin stimulus	Any process that activates or increases the frequency, rate or extent of cellular response to insulin stimulus.
	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:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0030278	regulation of ossification	Any process that modulates the frequency, rate or extent of bone formation.
	GO:0045667	regulation of osteoblast differentiation	Any process that modulates the frequency, rate or extent of osteoblast differentiation.
	GO:0045670	regulation of osteoclast differentiation	Any process that modulates the frequency, rate or extent of osteoclast differentiation.
	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:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	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:0045171	intercellular bridge	A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised.
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.

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	3k6p
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	ERR1_HUMAN \| P11474
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	ERR1_HUMAN \| P11474
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	ERR1_HUMAN \| P11474	:	1xb7 2pjl 3d24

(no "Related Entries Specified in the PDB File" available for 3K6P)

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Ligands, Modified Residues, Ions (1, 1)

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