4E2J - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF THE ANCESTRAL GLUCOCORTICOID RECEPTOR 2 LIGAND BINDING DOMAIN IN COMPLEX WITH MOMETASONE FUROATE AND TIF-2 COACTIVATOR FRAGMENT

Authors :   J. A. Kohn, K. Deshpande, E. A. Ortlund

Date :   08 Mar 12 (Deposition) - 28 Mar 12 (Release) - 30 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Nuclear Receptor Ligand Binding Domain, Glucocorticoid Receptor, Steroid Binding Protein, Hormone-Hormone Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Kohn, K. Deshpande, E. A. Ortlund
Deciphering Modern Glucocorticoid Cross-Pharmacology Using Ancestral Corticosteroid Receptors.
J. Biol. Chem. V. 287 16267 2012
PubMed-ID: 22437833 | Reference-DOI: 10.1074/JBC.M112.346411

Molecule 1 - ANCESTRAL GLUCOCORTICOID RECEPTOR 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	LIGAND BINDING DOMAIN
	Mutation	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	ANCESTRAL GENE RECONSTRUCTION

Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 2
	Chains	:	C, E
	Engineered	:	YES
	Fragment	:	NUCLEAR RECEPTOR BOX 3, UNP RESIDUES 741-752
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	NR BOX 3 FRAGMENT SYNTHESIZED BY RSSYNTHESIS.
	Synonym	:	NCOA-2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75, BHLHE75, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2, HTIF2
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	E
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	MOF	2	Ligand/Ion	MOMETASONE FUROATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	MOF	1	Ligand/Ion	MOMETASONE FUROATE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	MOF	1	Ligand/Ion	MOMETASONE FUROATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:37 , ARG A:38 , PRO A:219 , GLU A:220 , MET A:221 , HOH A:424 , TYR E:747	BINDING SITE FOR RESIDUE GOL A 301
2	AC2	SOFTWARE	LEU A:32 , ASN A:33 , GLY A:36 , GLN A:39 , ARG A:80 , PHE A:92 , MET A:108 , GLN A:111 , MET A:115 , PHE A:204 , CYS A:205 , THR A:208 , PHE A:218	BINDING SITE FOR RESIDUE MOF A 302
3	AC3	SOFTWARE	MET B:29 , LEU B:32 , ASN B:33 , GLY B:36 , GLN B:39 , ARG B:80 , PHE B:92 , MET B:108 , MET B:115 , PHE B:204 , CYS B:205 , THR B:208	BINDING SITE FOR RESIDUE MOF B 301
4	AC4	SOFTWARE	TYR B:67 , SER B:68 , TRP B:69 , MET B:70 , SER B:71 , LEU B:202	BINDING SITE FOR RESIDUE FMT B 302
5	AC5	SOFTWARE	ARG A:54	BINDING SITE FOR RESIDUE GOL B 303

(no "SS Bond" information available for 4E2J)

(no "Cis Peptide Bond" information available for 4E2J)

(no "SAP(SNP)/Variant" information available for 4E2J)

(no "PROSITE Motif" information available for 4E2J)

(no "Exon" information available for 4E2J)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e2j A  -1 PTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSSVEFPEMLAEIISNQLPKFKAGSVKPLLFHQ 245
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    || 219       229       239      
                                                                                                                                                                                                                                                213|                              
                                                                                                                                                                                                                                                 215

Chain B from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e2j B  -1 PTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGSVKPLLFHQ 245
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238

Chain C from PDB  Type:PROTEIN  Length:11
 aligned with NCOA2_HUMAN | Q15596 from UniProtKB/Swiss-Prot  Length:1464

    Alignment length:11
                                   751 
          NCOA2_HUMAN   742 NALLRYLLDKD 752
               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
                 4e2j C 742 NALLRYLLDKD 752
                                   751

Chain E from PDB  Type:PROTEIN  Length:12
 aligned with NCOA2_HUMAN | Q15596 from UniProtKB/Swiss-Prot  Length:1464

    Alignment length:12
                                   750  
          NCOA2_HUMAN   741 ENALLRYLLDKD 752
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4e2j E 741 ENALLRYLLDKD 752
                                   750

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 '\|'

(no "SCOP Domain" information available for 4E2J)

(no "CATH Domain" information available for 4E2J)

(no "Pfam Domain" information available for 4E2J)

Asymmetric Unit(hide GO term definitions)

Chain C,E (NCOA2_HUMAN | Q15596)

molecular function
	GO:0070182	DNA polymerase binding	Interacting selectively and non-covalently with a DNA polymerase.
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	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:0001162	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0030331	estrogen receptor binding	Interacting selectively and non-covalently with an estrogen receptor.
	GO:0035259	glucocorticoid receptor binding	Interacting selectively and non-covalently with a glucocorticoid receptor.
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	GO:0016922	ligand-dependent nuclear receptor binding	Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
	GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
	GO:0035257	nuclear hormone receptor binding	Interacting selectively and non-covalently with a nuclear hormone receptor, a ligand-dependent receptor found in the nucleus of the cell.
	GO:0033142	progesterone receptor binding	Interacting selectively and non-covalently with a progesterone receptor.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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: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:0046965	retinoid X receptor binding	Interacting selectively and non-covalently with a retinoid X receptor.
	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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0015721	bile acid and bile salt transport	The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0044255	cellular lipid metabolic process	The chemical reactions and pathways involving lipids, as carried out by individual cells.
	GO:1904017	cellular response to Thyroglobulin triiodothyronine	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 Thyroglobulin triiodothyronine stimulus.
	GO:0032870	cellular response to hormone stimulus	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 hormone stimulus.
	GO:0021549	cerebellum development	The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
	GO:0032922	circadian regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0045475	locomotor rhythm	The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
	GO:0008584	male gonad development	The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
	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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045925	positive regulation of female receptivity	Any process that activates or increases the receptiveness of a female to male advances.
	GO:2000324	positive regulation of glucocorticoid receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of glucocorticoid receptor signaling pathway.
	GO:2000273	positive regulation of receptor activity	Any process that activates or increases the frequency, rate or extent of receptor activity.
	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:0010906	regulation of glucose metabolic process	Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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.
	GO:0014069	postsynaptic density of dendrite	An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
	GO:0048786	presynaptic active zone	A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.
	GO:0005791	rough endoplasmic reticulum	The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

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