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P13053 (VDR_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 133. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Vitamin D3 receptor

Short name=VDR
Alternative name(s):
1,25-dihydroxyvitamin D3 receptor
Nuclear receptor subfamily 1 group I member 1
Gene names
Name:Vdr
Synonyms:Nr1i1
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length423 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis. Ref.5

Subunit structure

Homodimer in the absence of bound vitamin D3. Heterodimer with RXRA after vitamin D3 binding. Interacts with SMAD3. Interacts with MED1, NCOA1, NCOA2, NCOA3 and NCOA6 coactivators, leading to a strong increase of transcription of target genes. Interacts (in a ligand-dependent manner) with BAZ1B/WSTF. Interacts with SNW1. Interacts with IRX4, the interaction doesn't affect its transactivation activity By similarity. Ref.3

Subcellular location

Nucleus.

Tissue specificity

Detected in intestine and kidney. Ref.1

Domain

Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionReceptor
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processaging

Inferred from expression pattern PubMed 18060514. Source: RGD

apoptotic signaling pathway

Inferred from direct assay PubMed 9579411. Source: RGD

cellular response to vitamin D

Inferred from expression pattern PubMed 9753201. Source: RGD

heart development

Inferred from expression pattern PubMed 12107506. Source: RGD

regulation of calcium ion transport

Inferred from direct assay PubMed 18353900. Source: RGD

regulation of transcription from RNA polymerase II promoter

Traceable author statement PubMed 9579411. Source: RGD

response to calcium ion

Inferred from expression pattern PubMed 20181667. Source: RGD

response to estradiol

Inferred from expression pattern PubMed 10724336. Source: RGD

vitamin D receptor signaling pathway

Inferred from direct assay PubMed 9579411. Source: GOC

   Cellular_componentT-tubule

Inferred from direct assay PubMed 20015453. Source: RGD

cytosol

Inferred from direct assay PubMed 18060514. Source: RGD

dense fibrillar component

Inferred from direct assay PubMed 8392883. Source: RGD

euchromatin

Inferred from direct assay PubMed 8392883. Source: RGD

heterochromatin

Inferred from direct assay PubMed 8392883. Source: RGD

intracellular membrane-bounded organelle

Inferred from direct assay PubMed 18060514. Source: RGD

nuclear heterochromatin

Inferred from direct assay PubMed 12717384. Source: RGD

nuclear matrix

Inferred from direct assay PubMed 9744521. Source: RGD

perinuclear region of cytoplasm

Inferred from direct assay PubMed 9220147. Source: RGD

   Molecular_functioncalcitriol binding

Inferred from direct assay PubMed 8179318. Source: RGD

calcitriol receptor activity

Inferred from direct assay PubMed 9579411. Source: RGD

protein binding

Inferred from physical interaction. Source: BHF-UCL

sequence-specific DNA binding

Inferred from direct assay PubMed 16481392. Source: RGD

sequence-specific DNA binding transcription factor activity

Traceable author statement PubMed 11964167. Source: RGD

steroid hormone receptor activity

Inferred from electronic annotation. Source: InterPro

vitamin D binding

Inferred from direct assay Ref.2. Source: RGD

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 423423Vitamin D3 receptor
PRO_0000053544

Regions

DNA binding24 – 8966Nuclear receptor
Zinc finger24 – 4421NR C4-type
Zinc finger60 – 8425NR C4-type
Region90 – 18798Hinge
Region188 – 423236Ligand-binding
Region223 – 23311Vitamin D3 binding
Region242 – 26019Interaction with coactivator LXXLL motif
Region267 – 2748Vitamin D3 binding

Sites

Binding site1431Vitamin D3
Binding site3011Vitamin D3
Binding site3931Vitamin D3

Secondary structure

.................................... 423
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P13053 [UniParc].

Last modified January 1, 1990. Version 1.
Checksum: 1A0E519A9DCCE990

FASTA42347,814
        10         20         30         40         50         60 
MEATAASTSL PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR SMKRKALFTC 

        70         80         90        100        110        120 
PFNGDCRITK DNRRHCQACR LKRCVDIGMM KEFILTDEEV QRKREMIMKR KEEEALKDSL 

       130        140        150        160        170        180 
RPKLSEEQQH IIAILLDAHH KTYDPTYADF RDFRPPVRMD GSTGSYSPRP TLSFSGNSSS 

       190        200        210        220        230        240 
SSSDLYTTSL DMMEPSGFSN LDLNGEDSDD PSVTLDLSPL SMLPHLADLV SYSIQKVIGF 

       250        260        270        280        290        300 
AKMIPGFRDL TSDDQIVLLK SSAIEVIMLR SNQSFTMDDM SWDCGSQDYK YDVTDVSKAG 

       310        320        330        340        350        360 
HTLELIEPLI KFQVGLKKLN LHEEEHVLLM AICIVSPDRP GVQDAKLVEA IQDRLSNTLQ 

       370        380        390        400        410        420 
TYIRCRHPPP GSHQLYAKMI QKLADLRSLN EEHSKQYRSL SFQPENSMKL TPLVLEVFGN 


EIS 

« Hide

References

[1]"Structure and regulation of the rat 1,25-dihydroxyvitamin D3 receptor."
Burmester J.K., Wiese R.J., Maeda N., Deluca H.
Proc. Natl. Acad. Sci. U.S.A. 85:9499-9502(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
[2]"Isolation and expression of rat 1,25-dihydroxyvitamin D3 receptor cDNA."
Burmester J.K., Maeda N., Deluca H.F.
Proc. Natl. Acad. Sci. U.S.A. 85:1005-1009(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 58-423.
Tissue: Kidney.
[3]"A new family of nuclear receptor coregulators that integrates nuclear receptor signaling through CBP."
Mahajan M.A., Samuels H.H.
Mol. Cell. Biol. 20:5048-5063(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NCOA6.
[4]"Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide."
Vanhooke J.L., Benning M.M., Bauer C.B., Pike J.W., DeLuca H.F.
Biochemistry 43:4101-4110(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 116-423 IN COMPLEXES WITH VITAMIN D3 ANALOGS AND MED1.
[5]"New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 with conformationally restricted side chains: evaluation of biological activity and structural determination of VDR-bound conformations."
Vanhooke J.L., Tadi B.P., Benning M.M., Plum L.A., DeLuca H.F.
Arch. Biochem. Biophys. 460:161-165(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF 116-423 IN COMPLEXES WITH VITAMIN D3 ANALOGS AND MED1, FUNCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J04147 mRNA. Translation: AAA41089.1.
PIRA31761.
RefSeqNP_058754.1. NM_017058.1.
UniGeneRn.10911.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1RJKX-ray1.99A116-423[»]
1RK3X-ray2.20A116-423[»]
1RKGX-ray1.90A116-423[»]
1RKHX-ray2.28A116-423[»]
2O4JX-ray1.74A116-423[»]
2O4RX-ray1.98A116-423[»]
2ZFXX-ray1.99A116-423[»]
2ZL9X-ray1.90A116-423[»]
2ZLAX-ray2.00A116-423[»]
2ZLCX-ray2.00A116-423[»]
2ZMHX-ray2.10A116-423[»]
2ZMIX-ray1.70A116-423[»]
2ZMJX-ray2.35A116-423[»]
2ZXMX-ray3.01A116-423[»]
2ZXNX-ray2.10A116-423[»]
3A2HX-ray2.50A116-423[»]
3AFRX-ray2.00A116-423[»]
3AUNX-ray1.81A116-423[»]
3VJSX-ray1.93A116-423[»]
3VJTX-ray2.00A116-423[»]
3VRTX-ray2.40A116-423[»]
3VRUX-ray2.00A116-423[»]
3VRVX-ray1.90A116-423[»]
3VRWX-ray2.40A116-423[»]
3VT3X-ray1.70A116-423[»]
3VT4X-ray1.90A116-423[»]
3VT5X-ray2.11A116-423[»]
3VT6X-ray2.30A116-423[»]
3VT7X-ray1.65A116-423[»]
3VT8X-ray2.10A116-423[»]
3VT9X-ray2.35A116-423[»]
3VTBX-ray2.00A116-423[»]
3VTCX-ray1.50A116-423[»]
3VTDX-ray2.70A116-423[»]
3W0GX-ray1.94A121-420[»]
3W0HX-ray1.80A118-420[»]
3W0IX-ray1.90A121-420[»]
3W0JX-ray1.84A121-420[»]
3W5PX-ray1.90A116-423[»]
3W5QX-ray1.90A116-423[»]
3W5RX-ray2.20A116-423[»]
3W5TX-ray2.29A116-423[»]
ProteinModelPortalP13053.
SMRP13053. Positions 22-106, 118-421.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid246986. 5 interactions.
MINTMINT-236433.
STRING10116.ENSRNOP00000011601.

Chemistry

BindingDBP13053.
ChEMBLCHEMBL3150.
GuidetoPHARMACOLOGY605.

PTM databases

PhosphoSiteP13053.

Proteomic databases

PaxDbP13053.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID24873.
KEGGrno:24873.
UCSCRGD:3959. rat.

Organism-specific databases

CTD7421.
RGD3959. Vdr.

Phylogenomic databases

eggNOGNOG283526.
HOGENOMHOG000220844.
HOVERGENHBG108655.
InParanoidP13053.
KOK08539.
PhylomeDBP13053.

Gene expression databases

GenevestigatorP13053.

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.
IPR001723. Str_hrmn_rcpt.
IPR000324. VitD_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR00398. STRDHORMONER.
PR00047. STROIDFINGER.
PR00350. VITAMINDR.
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

EvolutionaryTraceP13053.
NextBio604698.
PROP13053.

Entry information

Entry nameVDR_RAT
AccessionPrimary (citable) accession number: P13053
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: June 11, 2014
This is version 133 of the entry and version 1 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