2E2R - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN ESTROGEN-RELATED RECEPTOR GAMMA LIGAND BINDING DOMAIN COMPLEX WITH BISPHENOL A

Authors :   A. Matsushima, Y. Kakuta, T. Teramoto, T. Koshiba, M. Kimura, Y. Shimoh

Date :   16 Nov 06 (Deposition) - 11 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Err Gamma, Bpa, Nuclear Receptor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Matsushima, Y. Kakuta, T. Teramoto, T. Koshiba, X. Liu, H. Okada, T. Tokunaga, S. Kawabata, M. Kimura, Y. Shimohigashi
Structural Evidence For Endocrine Disruptor Bisphenol A Binding To Human Nuclear Receptor Err{Gamma}
J. Biochem. (Tokyo) V. 142 517 2007
PubMed-ID: 17761695 | Reference-DOI: 10.1093/JB/MVM158

Molecule 1 - ESTROGEN-RELATED RECEPTOR GAMMA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN, RESIDUES 232-459
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ESTROGEN RECEPTOR-RELATED PROTEIN 3, ERR GAMMA-2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	2OH	1	Ligand/Ion	4,4'-PROPANE-2,2-DIYLDIPHENOL
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	2OH	2	Ligand/Ion	4,4'-PROPANE-2,2-DIYLDIPHENOL
2	GOL	6	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:268 , ALA A:272 , GLU A:275 , MET A:306 , LEU A:309 , ARG A:316 , TYR A:326 , LEU A:345 , ASN A:346 , ILE A:349 , PHE A:435	BINDING SITE FOR RESIDUE 2OH A 1401
2	AC2	SOFTWARE	LYS A:439 , GLY A:442 , VAL A:444 , PRO A:445 , MET A:446 , HOH A:1600 , HOH A:1625	BINDING SITE FOR RESIDUE GOL A 501
3	AC3	SOFTWARE	ASP A:322 , GLU A:323 , LEU A:324 , MET A:332 , ASP A:333 , GLU A:334 , SER A:337 , LEU A:343 , ASN A:346 , ASN A:347 , LEU A:350 , HOH A:1630	BINDING SITE FOR RESIDUE GOL A 502
4	AC4	SOFTWARE	GLU A:247 , LYS A:248 , TYR A:250 , LYS A:390 , VAL A:394 , HOH A:1624 , HOH A:1705 , HOH A:1735 , HOH A:1752	BINDING SITE FOR RESIDUE GOL A 503

(no "SS Bond" information available for 2E2R)

(no "Cis Peptide Bond" information available for 2E2R)

(no "SAP(SNP)/Variant" information available for 2E2R)

(no "PROSITE Motif" information available for 2E2R)

(no "Exon" information available for 2E2R)

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:228
 aligned with ERR3_HUMAN | P62508 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:228
                                                                                                                                                                                                                                                            458 
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      | 
           ERR3_HUMAN   232 KPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAKV-   -
               SCOP domains d2e2ra_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2e2rA00 A:232-459 Retinoid X Receptor                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeehhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2e2r A 232 KPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAKVC 459
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

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: automated matches (140)

Human (Homo sapiens) [TaxId: 9606] (122)

d2e2ra_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Retinoid X Receptor (409)

Homologous Superfamily: Retinoid X Receptor (409)

Human (Homo sapiens) (337)

2e2rA00

A:232-459

(no "Pfam Domain" information available for 2E2R)

Asymmetric Unit(hide GO term definitions)

Chain A (ERR3_HUMAN | P62508)

molecular function
	GO:0050682	AF-2 domain binding	Interacting selectively and non-covalently with the AF-2 domain of a protein, a highly conserved ligand-dependent transactivation domain which is essential for receptor-mediated transcriptional activation.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron 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:0003708	retinoic acid receptor activity	Combining with retinoic acid 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. Retinoic acid is one of the forms of vitamin A.
	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:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region 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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048384	retinoic acid receptor signaling pathway	The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
	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: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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