1OT7 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR 3-DEOXY-CDCA BINDING AND ACTIVATION OF FXR

Authors :   L. Z. Mi, S. Devarakonda, J. M. Harp, Q. Han, R. Pellicciari, T. M. Willson, S. Khorasanizadeh, F. Rastinejad

Date :   21 Mar 03 (Deposition) - 23 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Bile Acid, Nuclear Receptor, Coactivator, Ligand Binding Domain, Fxr, Hormone/Growth Factor Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Z. Mi, S. Devarakonda, J. M. Harp, Q. Han, R. Pellicciari, T. M. Willson, S. Khorasanizadeh, F. Rastinejad
Structural Basis For Bile Acid Binding And Activation Of The Nuclear Receptor Fxr
Mol. Cell V. 11 1093 2003
PubMed-ID: 12718893 | Reference-DOI: 10.1016/S1097-2765(03)00112-6
(for further references see the PDB file header)

Molecule 1 - BILE ACID RECEPTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	NR1H4
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	FXR

Molecule 2 - DODECAMER PEPTIDE FRAGMENT OF RPGR-INTERACTING PROTEIN 1
	Chains	:	C, D, E
	Engineered	:	YES
	Fragment	:	GRIP1 NID3
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CHC	1	Ligand/Ion	6-ETHYL-CHENODEOXYCHOLIC ACID
2	IU5	1	Ligand/Ion	ISO-URSODEOXYCHOLIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CHC	1	Ligand/Ion	6-ETHYL-CHENODEOXYCHOLIC ACID
2	IU5	-1	Ligand/Ion	ISO-URSODEOXYCHOLIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CHC	-1	Ligand/Ion	6-ETHYL-CHENODEOXYCHOLIC ACID
2	IU5	1	Ligand/Ion	ISO-URSODEOXYCHOLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET B:287 , ALA B:288 , HIS B:291 , MET B:325 , PHE B:326 , ARG B:328 , SER B:329 , ILE B:332 , PHE B:333 , ILE B:349 , TYR B:358 , TYR B:366 , HIS B:444	BINDING SITE FOR RESIDUE IU5 B 1002
2	AC2	SOFTWARE	MET A:262 , ALA A:288 , HIS A:291 , PHE A:326 , ARG A:328 , SER A:329 , ILE A:332 , ILE A:349 , TYR A:358 , PHE A:363 , TYR A:366 , HIS A:444	BINDING SITE FOR RESIDUE CHC A 1001

(no "SS Bond" information available for 1OT7)

Asymmetric Unit

No.	Residues
1	Asn A:423	-	Pro A:424

(no "SAP(SNP)/Variant" information available for 1OT7)

(no "PROSITE Motif" information available for 1OT7)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000009910	1	ENSRNOE00000353369	chr7:26307061-26306959	103	NR1H4_RAT	-	0	0	-	-
1.2	ENSRNOT00000009910	2	ENSRNOE00000069662	chr7:26276740-26276606	135	NR1H4_RAT	1-23	23	0	-	-
1.4	ENSRNOT00000009910	4	ENSRNOE00000066613	chr7:26258318-26257950	369	NR1H4_RAT	23-146	124	0	-	-
1.5a	ENSRNOT00000009910	5a	ENSRNOE00000336037	chr7:26240305-26240165	141	NR1H4_RAT	146-193	48	0	-	-
1.6	ENSRNOT00000009910	6	ENSRNOE00000066952	chr7:26237700-26237567	134	NR1H4_RAT	193-237	45	0	-	-
1.7	ENSRNOT00000009910	7	ENSRNOE00000067172	chr7:26235927-26235829	99	NR1H4_RAT	238-270	33	2	A:240-270 B:240-270	31 31
1.8	ENSRNOT00000009910	8	ENSRNOE00000067330	chr7:26235495-26235396	100	NR1H4_RAT	271-304	34	2	A:271-304 B:271-304	34 34
1.9	ENSRNOT00000009910	9	ENSRNOE00000067481	chr7:26230774-26230628	147	NR1H4_RAT	304-353	50	2	A:304-353 B:304-353	50 50
1.10	ENSRNOT00000009910	10	ENSRNOE00000067646	chr7:26191941-26191828	114	NR1H4_RAT	353-391	39	2	A:353-391 B:353-391	39 39
1.11	ENSRNOT00000009910	11	ENSRNOE00000342572	chr7:26190485-26189759	727	NR1H4_RAT	391-469	79	2	A:391-468 B:391-468	78 78

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
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Chain A from PDB  Type:PROTEIN  Length:229
 aligned with NR1H4_RAT | Q62735 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:229
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
            NR1H4_RAT   240 TELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
               SCOP domains d1ot7a_ A: Bile acid receptor FXR                                                                                                                                                                                                     SCOP domains
               CATH domains 1ot7A00 A:240-468 Retinoid X Receptor                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:240-270       Exon 1.8  PDB: A:271-304          ------------------------------------------------Exon 1.10  PDB: A:353-391              ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.9  PDB: A:304-353 UniProt: 304-353         -------------------------------------Exon 1.11  PDB: A:391-468 UniProt: 391-469 [INCOMPLETE]                        Transcript 1 (2)
                 1ot7 A 240 TELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459

Chain B from PDB  Type:PROTEIN  Length:229
 aligned with NR1H4_RAT | Q62735 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:229
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
            NR1H4_RAT   240 TELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
               SCOP domains d1ot7b_ B: Bile acid receptor FXR                                                                                                                                                                                                     SCOP domains
               CATH domains 1ot7B00 B:240-468 Retinoid X Receptor                                                                                                                                                                                                 CATH domains
           Pfam domains (1) --Hormone_recep-1ot7B01 B:242-461                                                                                                                                                                                             ------- Pfam domains (1)
           Pfam domains (2) --Hormone_recep-1ot7B02 B:242-461                                                                                                                                                                                             ------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: B:240-270       Exon 1.8  PDB: B:271-304          ------------------------------------------------Exon 1.10  PDB: B:353-391              ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.9  PDB: B:304-353 UniProt: 304-353         -------------------------------------Exon 1.11  PDB: B:391-468 UniProt: 391-469 [INCOMPLETE]                        Transcript 1 (2)
                 1ot7 B 240 TELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 468
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459

Chain C from PDB  Type:PROTEIN  Length:12
                                            
               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
                 1ot7 C   1 ENALLRYLLDKD  12
                                    10

Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1ot7 D   1 ENALLRYLLDKD  12
                                    10

Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1ot7 E   1 ENALLRYLLDKD  12
                                    10

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(

)

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: Bile acid receptor FXR (9)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

1a	d1ot7a_	A:
1b	d1ot7b_	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)

Norway rat (Rattus norvegicus) (18)

1a	1ot7A00	A:240-468
1b	1ot7B00	B:240-468

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Hormone_recep (290)

Rattus norvegicus (Rat) (22)

1a	Hormone_recep-1ot7B01	B:242-461
1b	Hormone_recep-1ot7B02	B:242-461

Asymmetric Unit(hide GO term definitions)

Chain A,B (NR1H4_RAT | Q62735)

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:0032052	bile acid binding	Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
	GO:0038181	bile acid receptor activity	Combining with a bile acid and transmitting the signal to initiate a change in cell activity. A bile acid is any member of a group of steroid carboxylic acids occurring in bile.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	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: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:0004887	thyroid hormone receptor activity	Combining with thyroid hormone 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: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:0008206	bile acid metabolic process	The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
	GO:0038183	bile acid signaling pathway	A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0048565	digestive tract development	The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	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: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:0006109	regulation of carbohydrate metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009749	response to glucose	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 a glucose stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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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