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P45446 (RORB_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nuclear receptor ROR-beta
Alternative name(s):
Nuclear receptor RZR-beta
Nuclear receptor subfamily 1 group F member 2
Retinoid-related orphan receptor-beta
Gene names
Name:Rorb
Synonyms:Nr1f2, Rzrb
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length470 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Nuclear receptor that binds DNA as a monomer to ROR response elements (RORE) containing a single core motif half-site 5'-AGGTCA-3' preceded by a short A-T-rich sequence. Considered to have intrinsic transcriptional activity, have some natural ligands such as all-trans retinoic acid (ATRA) and other retinoids which act as inverse agonists repressing the transcriptional activity. Required for normal postnatal development of rod and cone photoreceptor cells. Modulates rod photoreceptors differentiation at least by inducing the transcription factor NRL-mediated pathway. In cone photoreceptor cells, regulates transcription of OPN1SW. Involved in the regulation of the period length and stability of the circadian rhythm. May control cytoarchitectural patterning of neocortical neurons during development. May act in a dose-dependent manner to regulate barrel formation upon innervation of layer IV neurons by thalamocortical axons. May play a role in the suppression of osteoblastic differentiation through the inhibition of RUNX2 transcriptional activity. Ref.2 Ref.3 Ref.6

Isoform 1:Critical for hindlimb motor control and for the differentiation of amacrine and horizontal cells in the retina. Regulates the expression of PTF1A synergistically with FOXN4 By similarity. Ref.2 Ref.3 Ref.6

Subunit structure

Monomer. Interacts with CRX. Ref.3

Subcellular location

Nucleus By similarity.

Tissue specificity

Isoform 2 expressed with circadian rhythm in eye and pineal gland. Isoform 1 expressed in retina cortex, thalamus, and hypothalamus. Ref.2 Ref.4

Induction

Isoform 2 oscillates diurnally in eye and pineal gland, with highest levels shortly after midnight. Ref.2

Domain

AF-2 (activation function-2) motif is required for recruiting coregulators containing the LXXLL motif, such as NCOA1, and control the transactivational activity (Ref.3 and Ref.5). Ref.3 Ref.5

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Sequence caution

The sequence AAA42095.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processBiological rhythms
Sensory transduction
Transcription
Transcription regulation
Vision
   Cellular componentNucleus
   Coding sequence diversityAlternative promoter usage
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionActivator
Developmental protein
Receptor
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processG-protein coupled receptor signaling pathway

Inferred from direct assay PubMed 7961794. Source: GOC

amacrine cell differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

brain development

Inferred from expression pattern PubMed 8905729. Source: RGD

cellular response to retinoic acid

Inferred from direct assay Ref.6. Source: UniProtKB

circadian rhythm

Inferred from expression pattern PubMed 15781226PubMed 18321474. Source: RGD

eye photoreceptor cell development

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of osteoblast differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from direct assay Ref.2. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from direct assay Ref.6Ref.2. Source: UniProtKB

regulation of circadian rhythm

Inferred from sequence or structural similarity. Source: UniProtKB

response to hormone

Inferred from expression pattern PubMed 17067745. Source: RGD

retina development in camera-type eye

Inferred from sequence or structural similarity. Source: UniProtKB

retinal cone cell development

Inferred from sequence or structural similarity. Source: UniProtKB

retinal rod cell development

Inferred from sequence or structural similarity. Source: UniProtKB

visual perception

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity

Inferred from electronic annotation. Source: InterPro

melatonin receptor activity

Inferred from direct assay PubMed 7961794. Source: RGD

sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from direct assay Ref.6Ref.2. Source: UniProtKB

steroid hormone receptor activity

Inferred from electronic annotation. Source: InterPro

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative promoter usage. [Align] [Select]
Isoform 2 (identifier: P45446-2)

Also known as: ROR-beta 2;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Note: Shows a 4-fold higher transcriptional activation of an optimal promoter compared to isoform 1.
Isoform 1 (identifier: P45446-1)

Also known as: ROR-beta 1;

The sequence of this isoform differs from the canonical sequence as follows:
     1-13: MCENQLKTKADGT → MR

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 470470Nuclear receptor ROR-beta
PRO_0000053516

Regions

DNA binding18 – 9376Nuclear receptor Ref.2 Ref.3
Zinc finger21 – 4121NR C4-type
Zinc finger57 – 8125NR C4-type
Region94 – 211118Hinge Potential
Region222 – 470249Ligand-binding
Motif456 – 4616AF-2

Natural variations

Alternative sequence1 – 1313MCENQ…KADGT → MR in isoform 1.
VSP_022577

Experimental info

Mutagenesis2801A → F, V or S: Inhibits transactivation activity. Ref.5
Mutagenesis2801A → G: No effect on transactivation activity. Ref.5
Mutagenesis4571Y → A: Inhibits transactivation activity. Ref.5
Mutagenesis4591E → A: Inhibits transactivation activity. Ref.5

Secondary structure

.................................. 470
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 2 (ROR-beta 2) [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: FC31D327410FF310

FASTA47053,201
        10         20         30         40         50         60 
MCENQLKTKA DGTAQIEVIP CKICGDKSSG IHYGVITCEG CKGFFRRSQQ NNASYSCPRQ 

        70         80         90        100        110        120 
RNCLIDRTNR NRCQHCRLQK CLALGMSRDA VKFGRMSKKQ RDSLYAEVQK HQQRLQEQRQ 

       130        140        150        160        170        180 
QQSGEAEALA RVYSSSISNG LSNLNTETGG TYANGHVIDL PKSEGYYNID SGQPSPDQSG 

       190        200        210        220        230        240 
LDMTGIKQIK QEPIYDLTSV HNLFTYSSFN NGQLAPGITM SEIDRIAQNI IKSHLETCQY 

       250        260        270        280        290        300 
TMEELHQLAW QTHTYEEIKA YQSKSREALW QQCAIQITHA IQYVVEFAKR ITGFMELCQN 

       310        320        330        340        350        360 
DQILLLKSGC LEVVLVRMCR AFNPLNNTVL FEGKYGGMQM FKALGSDDLV NEAFDFAKNL 

       370        380        390        400        410        420 
CSLQLTEEEI ALFSSAVLIS PDRAWLLEPR KVQKLQEKIY FALQHVIQKN HLDDETLAKL 

       430        440        450        460        470 
IAKIPTITAV CNLHGEKLQV FKQSHPDIVN TLFPPLYKEL FNPDCAAVCK 

« Hide

Isoform 1 (ROR-beta 1) [UniParc].

Checksum: B415C0BDBA61D6D6
Show »

FASTA45952,068

References

[1]"RZRs, a new family of retinoid-related orphan receptors that function as both monomers and homodimers."
Carlberg C., Hooft van Huijsduijnen R., Staple J.K., Delamarter J.F., Becker-Andre M.
Mol. Endocrinol. 8:757-770(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
Strain: Sprague-Dawley.
Tissue: Brain.
[2]"A novel isoform of the orphan nuclear receptor RORbeta is specifically expressed in pineal gland and retina."
Andre E., Gawlas K., Becker-Andre M.
Gene 216:277-283(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION AS TRANSCRIPTION ACTIVATOR (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, DNA-BINDING, INDUCTION.
[3]"Functional analysis of retinoid Z receptor beta, a brain-specific nuclear orphan receptor."
Greiner E.F., Kirfel J., Greschik H., Doerflinger U., Becker P., Mercep A., Schuele R.
Proc. Natl. Acad. Sci. U.S.A. 93:10105-10110(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS TRANSCRIPTION MODULATOR, SUBUNIT, DNA-BINDING, DOMAIN.
[4]"Disruption of retinoid-related orphan receptor beta changes circadian behavior, causes retinal degeneration and leads to vacillans phenotype in mice."
Andre E., Conquet F., Steinmayr M., Stratton S.C., Porciatti V., Becker-Andre M.
EMBO J. 17:3867-3877(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
[5]"X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation."
Stehlin C., Wurtz J.-M., Steinmetz A., Greiner E., Schuele R., Moras D., Renaud J.-P.
EMBO J. 20:5822-5831(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 212-463 IN COMPLEX WITH STEARIC ACID AND NCOA1 PEPTIDE, DOMAIN, MUTAGENESIS OF ALA-280; TYR-457 AND GLU-459.
[6]"All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta."
Stehlin-Gaon C., Willmann D., Zeyer D., Sanglier S., van Dorsselaer A., Renaud J.-P., Moras D., Schule R.
Nat. Struct. Biol. 10:820-825(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 219-462 IN COMPLEX WITH RETINOIC ACID AND PEPTIDE SRC-1, FUNCTION AS TRANSCRIPTION ACTIVATOR, IDENTIFICATION OF LIGANDS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L14610 Genomic DNA. Translation: AAA42095.1. Different initiation.
PIRI65219.
UniGeneRn.231652.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1K4WX-ray1.90A212-463[»]
1N4HX-ray2.10A212-470[»]
1NQ7X-ray1.50A219-462[»]
ProteinModelPortalP45446.
SMRP45446. Positions 18-98, 219-462.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000018137.

PTM databases

PhosphoSiteP45446.

Proteomic databases

PaxDbP45446.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

UCSCRGD:1306778. rat. [P45446-2]

Organism-specific databases

RGD1306778. Rorb.

Phylogenomic databases

eggNOGNOG324222.
HOGENOMHOG000010200.
HOVERGENHBG106848.
InParanoidP45446.
PhylomeDBP45446.

Gene expression databases

GenevestigatorP45446.

Family and domain databases

Gene3D1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProIPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR003079. ROR_rcpt.
IPR001723. Str_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR01293. RORNUCRECPTR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMSSF48508. SSF48508. 1 hit.
PROSITEPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP45446.
PROP45446.

Entry information

Entry nameRORB_RAT
AccessionPrimary (citable) accession number: P45446
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 129 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references