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Title :   CRYSTAL STRUCTURE OF HUMAN ESTROGEN-RELATED RECEPTOR ALPHA IN COMPLEX WITH A SYNTHETIC INVERSE AGONIST REVEALS ITS NOVEL MOLECULAR MECHANISM

Authors :   J. Kallen

Date :   16 Apr 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Nuclear Hormone Receptor, Ligand Binding Domain, Ligand Binding Pocket, Three-Layered Alpha-Helical Sandwich, Inverse Agonist, Helix 12 (H12), Coactivator Groove, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kallen, R. Lattmann, R. Beerli, A. Blechschmidt, M. J. Blommers, M. Geiser, J. Ottl, J. M. Schlaeppi, A. Strauss, B. Fournier
Crystal Structure Of Human Estrogen-Related Receptor Alpha In Complex With A Synthetic Inverse Agonist Reveals Its Novel Molecular Mechanism.
J. Biol. Chem. V. 282 23231 2007
PubMed-ID: 17556356 | Reference-DOI: 10.1074/JBC.M703337200

Molecule 1 - STEROID HORMONE RECEPTOR ERR1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	ESRRA, ERR1, ESRL1, NR3B1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ESTROGEN-RELATED RECEPTOR, ALPHA, ERR- ALPHA, ESTROGEN RECEPTOR-LIKE 1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	047	2	Ligand/Ion	1-CYCLOHEXYL-N-{[1-(4-METHYLPHENYL)-1H-INDOL-3-YL]METHYL}METHANAMINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	047	6	Ligand/Ion	1-CYCLOHEXYL-N-{[1-(4-METHYLPHENYL)-1H-INDOL-3-YL]METHYL}METHANAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:5 , VAL A:321 , LEU A:324 , GLU A:331 , PHE A:382 , GLY A:397 , PHE A:495	BINDING SITE FOR RESIDUE 047 A 600
2	AC2	SOFTWARE	HOH B:11 , LEU B:324 , PHE B:328 , GLU B:331 , PHE B:382 , LEU B:386 , GLY B:397 , LEU B:398 , PHE B:495 , LEU B:500	BINDING SITE FOR RESIDUE 047 B 700

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

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

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

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

Asymmetric Unit (4, 8)

	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	2	A:282-288 (gaps) B:282-288 (gaps)	8 8
1.6a	ENST00000000442	6a	ENSE00001195335	chr11:64082213-64082383	171	ERR1_HUMAN	191-248	58	2	A:289-344 (gaps) B:289-344 (gaps)	56 56
1.7	ENST00000000442	7	ENSE00000727249	chr11:64082473-64082742	270	ERR1_HUMAN	248-338	91	2	A:344-434 B:344-434	91 91
1.8b	ENST00000000442	8b	ENSE00001271942	chr11:64083179-64084210	1032	ERR1_HUMAN	338-423	86	2	A:434-517 (gaps) B:434-517 (gaps)	84 84

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:218
 aligned with ERR1_HUMAN | P11474 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:255
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416     
           ERR1_HUMAN   167 VDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAM 421
               SCOP domains d2pj la_                   A: Steroid hormone          receptor ERR1                                                                                                                                                                                            SCOP domains
               CATH domains 2pjl A00                   A:282-517 Retinoid          X Receptor                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh-hhh------------------hhhhhhhhhhhh........---------..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeehhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. 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:434-517 (gaps) UniProt: 338-423 [INCOMPLETE]                       Transcript 1 (2)
                 2pjl A 282 LEVL-FQG------------------PVNALVSHLLVVEPEKLYAM---------LPAVATLSDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAG---------RRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAM 517
                               | | | -         -      |292       302     |   -     | 322       332       342       352       362       372       382       392       402       412       422       432       442       452        |-       472       482       492       502       512     
                             285 | |                289                308       318                                                                                                                                            461       471                                              
                               286 |                                                                                                                                                                                                                                                       
                                 288

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with ERR1_HUMAN | P11474 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:255
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416     
           ERR1_HUMAN   167 VDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAM 421
               SCOP domains d2pj lb_                   B: Steroid hormone          receptor ERR1                                                                                                                                                                                            SCOP domains
               CATH domains 2pjl B00                   B:282-517 Retinoid          X Receptor                                                                                                                                                                                               CATH domains
           Pfam domains (1) ---- ---                  --------------------         -Hormone_recep-2pjlB01 B:319-510                                                                                                                                                                 ------- Pfam domains (1)
           Pfam domains (2) ---- ---                  --------------------         -Hormone_recep-2pjlB02 B:319-510                                                                                                                                                                 ------- Pfam domains (2)
         Sec.struct. author .hhh-hhh------------------hhhhhhhhhhhh........---------..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..eeehhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5 UniProt: 148-191--------------------------------------------------------Exon 1.7  PDB: B:344-434 UniProt: 248-338                                                  ----------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.6a  PDB: B:289-344 (gaps) UniProt: 191-248         -----------------------------------------------------------------------------------------Exon 1.8b  PDB: B:434-517 (gaps) UniProt: 338-423 [INCOMPLETE]                       Transcript 1 (2)
                 2pjl B 282 LEVL-FQG------------------PVNALVSHLLVVEPEKLYAM---------LPAVATLSDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAG---------RRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAM 517
                               | | | -         -      |292       302     |   -     | 322       332       342       352       362       372       382       392       402       412       422       432       442       452        |-       472       482       492       502       512     
                             285 | |                289                308       318                                                                                                                                            461       471                                              
                               286 |                                                                                                                                                                                                                                                       
                                 288

Legend:		→ Mismatch	(orange background)
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	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( (-)

)

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: Steroid hormone receptor ERR1 (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d2pjla_	A:
1b	d2pjlb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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)

1a	2pjlA00	A:282-517
1b	2pjlB00	B:282-517

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Hormone_recep (290)

Homo sapiens (Human) (244)

1a	Hormone_recep-2pjlB01	B:319-510
1b	Hormone_recep-2pjlB02	B:319-510

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	2pjl
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	ERR1_HUMAN \| P11474	:	1xb7 3d24 3k6p

1xb7	X-RAY STRUCTURE OF APO ERRALPHA LBD IN COMPLEX WITH A PGC- 1ALPHA PEPTIDE AT 2.5A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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Exons (4, 8)

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