4A2J - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PR X-RAY STRUCTURES IN AGONIST CONFORMATIONS REVEAL TWO DIFFERENT MECHANISMS FOR PARTIAL AGONISM IN 11BETA-SUBSTITUTED STEROIDS

Authors :   S. J. Lusher, H. C. A. Raaijmakers, R. Bosch, D. Vu-Pham, R. Mcguire, A. O J. De Vlieg

Date :   27 Sep 11 (Deposition) - 04 Apr 12 (Release) - 04 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Transcription, Partial Agonist (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Lusher, H. C. A. Raaijmakers, D. Vu-Pham, B. Kazemier, R. Bosch, R. Mcguire, R. Azevedo, H. Hamersma, K. Dechering, A. Oubrie, M. Van Duin, J. De Vlieg
X-Ray Structures Of Progesterone Receptor Ligand Binding Domain In Its Agonist State Reveal Differing Mechanisms For Mixed Profiles Of 11Beta-Substituted Steroids.
J. Biol. Chem. V. 287 20333 2012
PubMed-ID: 22535964 | Reference-DOI: 10.1074/JBC.M111.308403

Molecule 1 - PROGESTERONE RECEPTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN, RESIDUES 514-769
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	AS0	2	Ligand/Ion	4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDEOXIME
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AS0	1	Ligand/Ion	4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDEOXIME
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AS0	1	Ligand/Ion	4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDEOXIME
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:715 , LEU A:718 , ASN A:719 , GLY A:722 , GLU A:723 , GLN A:725 , LEU A:726 , TRP A:755 , MET A:759 , ARG A:766 , PHE A:778 , PHE A:794 , LEU A:797 , MET A:801 , CYS A:891 , MET A:909	BINDING SITE FOR RESIDUE AS0 A1000
2	AC2	SOFTWARE	LEU B:715 , LEU B:718 , ASN B:719 , LEU B:721 , GLY B:722 , GLU B:723 , GLN B:725 , LEU B:726 , TRP B:755 , MET B:759 , ARG B:766 , PHE B:778 , MET B:801 , TYR B:890 , CYS B:891 , MET B:909	BINDING SITE FOR RESIDUE AS0 B1000
3	AC3	SOFTWARE	PRO A:737 , GLY A:738 , ARG A:740 , ASN A:741 , HOH A:2010	BINDING SITE FOR RESIDUE SO4 A1934

(no "SS Bond" information available for 4A2J)

(no "Cis Peptide Bond" information available for 4A2J)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014628	S	865	L	PRGR_HUMAN	Polymorphism	2020880	A/B	S	865	L

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014628	S	865	L	PRGR_HUMAN	Polymorphism	2020880	A	S	865	L

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014628	S	865	L	PRGR_HUMAN	Polymorphism	2020880	B	S	865	L

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

(no "PROSITE Motif" information available for 4A2J)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000325455	1a	ENSE00001204729	chr11:101001255-100998165	3091	PRGR_HUMAN	1-546	546	0	-	-
1.2	ENST00000325455	2	ENSE00000989714	chr11:100996889-100996738	152	PRGR_HUMAN	546-597	52	0	-	-
1.3	ENST00000325455	3	ENSE00000745002	chr11:100962607-100962491	117	PRGR_HUMAN	597-636	40	0	-	-
1.4b	ENST00000325455	4b	ENSE00000795216	chr11:100933483-100933178	306	PRGR_HUMAN	636-738	103	2	A:683-738 B:683-738	56 56
1.5a	ENST00000325455	5a	ENSE00000989716	chr11:100922299-100922155	145	PRGR_HUMAN	738-786	49	2	A:738-786 B:738-786	49 49
1.6a	ENST00000325455	6a	ENSE00000989717	chr11:100920790-100920660	131	PRGR_HUMAN	786-830	45	2	A:786-830 B:786-830	45 45
1.7a	ENST00000325455	7a	ENSE00000795215	chr11:100912833-100912676	158	PRGR_HUMAN	830-882	53	2	A:830-882 B:830-882	53 53
1.8d	ENST00000325455	8d	ENSE00001350778	chr11:100910002-100900355	9648	PRGR_HUMAN	883-933	51	2	A:883-932 B:883-932	50 50

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:250
 aligned with PRGR_HUMAN | P06401 from UniProtKB/Swiss-Prot  Length:933

    Alignment length:250
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932
           PRGR_HUMAN   683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
               SCOP domains d4a2ja_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: A:683-738 UniProt: 636-738 [INCOMPLETE] -----------------------------------------------Exon 1.6a  PDB: A:786-830 UniProt: 786-830   ----------------------------------------------------Exon 1.8d  PDB: A:883-932 UniProt: 883-933         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.5a  PDB: A:738-786 UniProt: 738-786       -------------------------------------------Exon 1.7a  PDB: A:830-882 UniProt: 830-882           -------------------------------------------------- Transcript 1 (2)
                 4a2j A 683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with PRGR_HUMAN | P06401 from UniProtKB/Swiss-Prot  Length:933

    Alignment length:250
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932
           PRGR_HUMAN   683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
               SCOP domains d4a2jb_ B: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:683-738 UniProt: 636-738 [INCOMPLETE] -----------------------------------------------Exon 1.6a  PDB: B:786-830 UniProt: 786-830   ----------------------------------------------------Exon 1.8d  PDB: B:883-932 UniProt: 883-933         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.5a  PDB: B:738-786 UniProt: 738-786       -------------------------------------------Exon 1.7a  PDB: B:830-882 UniProt: 830-882           -------------------------------------------------- Transcript 1 (2)
                 4a2j B 683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932

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)

1a	d4a2ja_	A:
1b	d4a2jb_	B:

(no "CATH Domain" information available for 4A2J)

(no "Pfam Domain" information available for 4A2J)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRGR_HUMAN | P06401)

molecular function
	GO:0051117	ATPase binding	Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
	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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0010629	negative regulation of gene expression	Any process that decreases 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: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: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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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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1a28	HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN
1e3k	HUMAN PROGESTERON RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITH THE LIGAND METRIBOLONE (R1881)
1sqn	PROGESTERONE RECEPTOR LIGAND BINDING DOMAIN WITH BOUNDNORETHINDRONE
1sr7	PROGESTERONE RECEPTOR HORMONE BINDING DOMAIN WITH BOUNDMOMETASONE FUROATE
1zuc	PROGESTERONE RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITHTHE NONSTEROIDAL AGONIST TANAPROGET
2c7a	STRUCTURE OF THE PROGESTERONE RECEPTOR-DNA COMPLEX
2w8y	RU486 BOUND TO THE PROGESTERONE RECEPTOR IN A DESTABILIZED AGONISTIC CONFORMATION
3zr7	STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM FOR A SET OF CHEMICALLY RELATED PROGESTERONE RECEPTOR MODULATORS
3zra	STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM FOR A SET OF CHEMICALLY RELATED PROGESTERONE RECEPTOR MODULATORS
3zrb	STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM FOR A SET OF CHEMICALLY RELATED PROGESTERONE RECEPTOR MODULATORS
4a2k	PR X-RAY STRUCTURES IN AGONIST CONFORMATIONS REVEAL TWO DIFFERENT MECHANISMS FOR PARTIAL AGONISM IN 11BETA- SUBSTITUTED STEROIDS
4apu	PR X-RAY STRUCTURES IN AGONIST CONFORMATIONS REVEAL TWO DIFFERENT MECHANISMS FOR PARTIAL AGONISM IN 11BETA- SUBSTITUTED STEROIDS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

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Exons (5, 10)

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SCOP Domains (1, 2)

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Gene Ontology (28, 28)

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