1HRA - JenaLib

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Title :   THE SOLUTION STRUCTURE OF THE HUMAN RETINOIC ACID RECEPTOR-BETA DNA-BINDING DOMAIN

Authors :   R. M. A. Knegtel, M. Katahira, J. G. Schilthuis, A. M. J. J. Bonvin, R. Boelens, D. Eib, P. T. Van Der Saag, R. Kaptein

Date :   25 Jul 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (15x)

Keywords :   Dna-Binding Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Knegtel, M. Katahira, J. G. Schilthuis, A. M. Bonvin, R. Boelens, D. Eib, P. T. Van Der Saag, R. Kaptein
The Solution Structure Of The Human Retinoic Acid Receptor-Beta Dna-Binding Domain.
J. Biomol. Nmr V. 3 1 1993
PubMed-ID: 8383553 | Reference-DOI: 10.1007/BF00242472
(for further references see the PDB file header)

Molecule 1 - RETINOIC ACID RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (15x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:8 , CYS A:11 , CYS A:25 , CYS A:28	BINDING SITE FOR RESIDUE ZN A 81
2	AC2	SOFTWARE	CYS A:44 , ARG A:46 , ASP A:47 , CYS A:50 , CYS A:60 , CYS A:63	BINDING SITE FOR RESIDUE ZN A 82

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

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15	Cys A:8	-	Phe A:9
2	1, 2, 3, 5, 6, 7, 8, 9, 12, 15	Cys A:11	-	Gln A:12
3	1, 2, 4, 5, 6, 7, 9, 10, 12, 13, 14, 15	Arg A:57	-	Asn A:58
4	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15	Val A:78	-	Arg A:79
5	2, 7, 9, 10, 11, 12, 13, 14, 15	Gly A:17	-	Tyr A:18
6	2	Lys A:38	-	Asn A:39
7	3	Arg A:3	-	Val A:4
8	3, 6	Asp A:13	-	Lys A:14
9	3, 4, 5, 7, 8, 10, 12, 13, 15	Cys A:44	-	His A:45
10	4, 8, 10, 14	Met A:1	-	Pro A:2
11	4	Ser A:15	-	Ser A:16
12	4, 5, 6, 7, 10, 12, 15	Thr A:43	-	Cys A:44
13	5	Pro A:2	-	Arg A:3
14	5, 13	Ile A:41	-	Tyr A:42
15	6	Val A:51	-	Ile A:52
16	8	Asn A:58	-	Arg A:59

NMR Structure (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	CancerSNP	VAR_RARB_HUMAN_CCDS2642_1_01 *	R	83	I	RARB_HUMAN	Disease (Colorectal cancer)	---	A	V	3	I
2	UniProt	VAR_036060	V	90	I	RARB_HUMAN	Unclassified	---	A	V	10	I
	* ID not provided by source

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

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUCLEAR_REC_DBD_2	PS51030	Nuclear hormone receptors DNA-binding domain profile.	RARB_HUMAN	85-160	1	A:5-80
2	NUCLEAR_REC_DBD_1	PS00031	Nuclear hormones receptors DNA-binding region signature.	RARB_HUMAN	88-114	1	A:8-34

(no "Exon" information available for 1HRA)

NMR Structure

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:80
 aligned with RARB_HUMAN | P10826 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:80
                                    90       100       110       120       130       140       150       160
           RARB_HUMAN    81 PPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVRN 160
               SCOP domains d1hraa_ A: Retinoic acid receptor DNA-binding domain                             SCOP domains
               CATH domains 1hraA00 A:1-80 Erythroid Transcription Factor GATA-1, subunit A                  CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhhh....................hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------I---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----NUCLEAR_REC_DBD_2  PDB: A:5-80 UniProt: 85-160                               PROSITE (1)
                PROSITE (2) -------NUCLEAR_REC_DBD_1          ---------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1hra A   1 MPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVRN  80
                                    10        20        30        40        50        60        70        80

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Small proteins (3458)

Fold: Glucocorticoid receptor-like (DNA-binding domain) (292)

Superfamily: Glucocorticoid receptor-like (DNA-binding domain) (292)

Family: Nuclear receptor (49)

Protein domain: Retinoic acid receptor DNA-binding domain (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1hraa_

NMR Structure

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Erythroid Transcription Factor GATA-1; Chain A (61)

Homologous Superfamily: Erythroid Transcription Factor GATA-1, subunit A (61)

Human (Homo sapiens) (8)

1hraA00

A:1-80

(no "Pfam Domain" information available for 1HRA)

NMR Structure(hide GO term definitions)

Chain A (RARB_HUMAN | P10826)

molecular function
	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:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	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: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: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:0046965	retinoid X receptor binding	Interacting selectively and non-covalently with a retinoid X receptor.
	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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0060348	bone development	The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
	GO:0048566	embryonic digestive tract development	The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
	GO:0048048	embryonic eye morphogenesis	The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
	GO:0035116	embryonic hindlimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
	GO:0002068	glandular epithelial cell development	The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
	GO:0003417	growth plate cartilage development	The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0061037	negative regulation of cartilage development	Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0032331	negative regulation of chondrocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
	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:0022008	neurogenesis	Generation of cells within the nervous system.
	GO:0003148	outflow tract septum morphogenesis	The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0045666	positive regulation of neuron differentiation	Any process that activates or increases the frequency, rate or extent of neuron differentiation.
	GO:0043068	positive regulation of programmed cell death	Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
	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:0031641	regulation of myelination	Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0060041	retina development in camera-type eye	The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
	GO:0003406	retinal pigment epithelium development	The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells.
	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: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:0021756	striatum development	The progression of the striatum over time from its initial formation until its mature state. The striatum is a region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.
	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.
	GO:0001657	ureteric bud development	The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
	GO:0055012	ventricular cardiac muscle cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a ventricular cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The ventricle is the part of the heart that pumps blood out of the organ.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

NMR Structure
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	Cis Peptide Bonds
		Arg A:3 - Val A:4	[ RasMol ]
		Arg A:57 - Asn A:58	[ RasMol ]
		Asn A:58 - Arg A:59	[ RasMol ]
		Asp A:13 - Lys A:14	[ RasMol ]
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		Cys A:44 - His A:45	[ RasMol ]
		Cys A:8 - Phe A:9	[ RasMol ]
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		Lys A:38 - Asn A:39	[ RasMol ]
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		Ser A:15 - Ser A:16	[ RasMol ]
		Thr A:43 - Cys A:44	[ RasMol ]
		Val A:51 - Ile A:52	[ RasMol ]
		Val A:78 - Arg A:79	[ RasMol ]

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	1hra
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	RARB_HUMAN \| P10826	:	1xap 4dm6 4dm8 4jyg 4jyh 4jyi

(no "Related Entries Specified in the PDB File" available for 1HRA)

Description

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