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P13053

- VDR_RAT

UniProt

P13053 - VDR_RAT

Protein

Vitamin D3 receptor

Gene

Vdr

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 1 (01 Jan 1990)
      Previous versions | rss
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    Functioni

    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.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei143 – 1431Vitamin D3
    Binding sitei301 – 3011Vitamin D3
    Binding sitei393 – 3931Vitamin D3

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi24 – 8966Nuclear receptorPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri24 – 4421NR C4-typePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri60 – 8425NR C4-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. calcitriol binding Source: RGD
    2. calcitriol receptor activity Source: RGD
    3. protein binding Source: RGD
    4. sequence-specific DNA binding Source: RGD
    5. sequence-specific DNA binding transcription factor activity Source: RGD
    6. steroid hormone receptor activity Source: InterPro
    7. vitamin D binding Source: RGD
    8. zinc ion binding Source: InterPro

    GO - Biological processi

    1. aging Source: RGD
    2. apoptotic signaling pathway Source: RGD
    3. cellular response to vitamin D Source: RGD
    4. heart development Source: RGD
    5. regulation of calcium ion transport Source: RGD
    6. regulation of transcription from RNA polymerase II promoter Source: RGD
    7. response to calcium ion Source: RGD
    8. response to estradiol Source: RGD
    9. vitamin D receptor signaling pathway Source: GOC

    Keywords - Molecular functioni

    Receptor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vitamin D3 receptor
    Short name:
    VDR
    Alternative name(s):
    1,25-dihydroxyvitamin D3 receptor
    Nuclear receptor subfamily 1 group I member 1
    Gene namesi
    Name:Vdr
    Synonyms:Nr1i1
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Unplaced

    Organism-specific databases

    RGDi3959. Vdr.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: RGD
    2. dense fibrillar component Source: RGD
    3. euchromatin Source: RGD
    4. heterochromatin Source: RGD
    5. intracellular membrane-bounded organelle Source: RGD
    6. nuclear heterochromatin Source: RGD
    7. nuclear matrix Source: RGD
    8. perinuclear region of cytoplasm Source: RGD
    9. T-tubule Source: RGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 423423Vitamin D3 receptorPRO_0000053544Add
    BLAST

    Proteomic databases

    PaxDbiP13053.

    PTM databases

    PhosphoSiteiP13053.

    Expressioni

    Tissue specificityi

    Detected in intestine and kidney.1 Publication

    Gene expression databases

    GenevestigatoriP13053.

    Interactioni

    Subunit structurei

    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.By similarity

    Protein-protein interaction databases

    BioGridi246986. 5 interactions.
    MINTiMINT-236433.
    STRINGi10116.ENSRNOP00000011601.

    Structurei

    Secondary structure

    1
    423
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi116 – 1194
    Helixi126 – 14217
    Helixi148 – 1525
    Turni219 – 2224
    Helixi223 – 24119
    Helixi247 – 2493
    Helixi252 – 27019
    Helixi271 – 2733
    Beta strandi274 – 2763
    Turni277 – 2804
    Beta strandi281 – 2833
    Helixi287 – 2893
    Beta strandi290 – 2923
    Helixi293 – 2975
    Turni298 – 3003
    Helixi303 – 31715
    Helixi323 – 33412
    Helixi345 – 36622
    Turni369 – 3746
    Helixi375 – 40127
    Helixi404 – 4074
    Helixi412 – 4187

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    3WT5X-ray1.90A116-423[»]
    3WT6X-ray2.00A116-423[»]
    3WT7X-ray2.40A116-423[»]
    ProteinModelPortaliP13053.
    SMRiP13053. Positions 22-106, 118-421.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13053.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni90 – 18798HingeAdd
    BLAST
    Regioni188 – 423236Ligand-bindingAdd
    BLAST
    Regioni223 – 23311Vitamin D3 bindingAdd
    BLAST
    Regioni242 – 26019Interaction with coactivator LXXLL motifAdd
    BLAST
    Regioni267 – 2748Vitamin D3 binding

    Domaini

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

    Sequence similaritiesi

    Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri24 – 4421NR C4-typePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri60 – 8425NR C4-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG283526.
    HOGENOMiHOG000220844.
    HOVERGENiHBG108655.
    InParanoidiP13053.
    KOiK08539.
    PhylomeDBiP13053.

    Family and domain databases

    Gene3Di1.10.565.10. 2 hits.
    3.30.50.10. 1 hit.
    InterProiIPR008946. 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]
    PfamiPF00104. Hormone_recep. 1 hit.
    PF00105. zf-C4. 1 hit.
    [Graphical view]
    PRINTSiPR00398. STRDHORMONER.
    PR00047. STROIDFINGER.
    PR00350. VITAMINDR.
    SMARTiSM00430. HOLI. 1 hit.
    SM00399. ZnF_C4. 1 hit.
    [Graphical view]
    SUPFAMiSSF48508. SSF48508. 1 hit.
    PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
    PS51030. NUCLEAR_REC_DBD_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P13053-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEATAASTSL PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR    50
    SMKRKALFTC PFNGDCRITK DNRRHCQACR LKRCVDIGMM KEFILTDEEV 100
    QRKREMIMKR KEEEALKDSL RPKLSEEQQH IIAILLDAHH KTYDPTYADF 150
    RDFRPPVRMD GSTGSYSPRP TLSFSGNSSS SSSDLYTTSL DMMEPSGFSN 200
    LDLNGEDSDD PSVTLDLSPL SMLPHLADLV SYSIQKVIGF AKMIPGFRDL 250
    TSDDQIVLLK SSAIEVIMLR SNQSFTMDDM SWDCGSQDYK YDVTDVSKAG 300
    HTLELIEPLI KFQVGLKKLN LHEEEHVLLM AICIVSPDRP GVQDAKLVEA 350
    IQDRLSNTLQ TYIRCRHPPP GSHQLYAKMI QKLADLRSLN EEHSKQYRSL 400
    SFQPENSMKL TPLVLEVFGN EIS 423
    Length:423
    Mass (Da):47,814
    Last modified:January 1, 1990 - v1
    Checksum:i1A0E519A9DCCE990
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J04147 mRNA. Translation: AAA41089.1.
    PIRiA31761.
    RefSeqiNP_058754.1. NM_017058.1.
    UniGeneiRn.10911.

    Genome annotation databases

    GeneIDi24873.
    KEGGirno:24873.
    UCSCiRGD:3959. rat.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J04147 mRNA. Translation: AAA41089.1 .
    PIRi A31761.
    RefSeqi NP_058754.1. NM_017058.1.
    UniGenei Rn.10911.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1RJK X-ray 1.99 A 116-423 [» ]
    1RK3 X-ray 2.20 A 116-423 [» ]
    1RKG X-ray 1.90 A 116-423 [» ]
    1RKH X-ray 2.28 A 116-423 [» ]
    2O4J X-ray 1.74 A 116-423 [» ]
    2O4R X-ray 1.98 A 116-423 [» ]
    2ZFX X-ray 1.99 A 116-423 [» ]
    2ZL9 X-ray 1.90 A 116-423 [» ]
    2ZLA X-ray 2.00 A 116-423 [» ]
    2ZLC X-ray 2.00 A 116-423 [» ]
    2ZMH X-ray 2.10 A 116-423 [» ]
    2ZMI X-ray 1.70 A 116-423 [» ]
    2ZMJ X-ray 2.35 A 116-423 [» ]
    2ZXM X-ray 3.01 A 116-423 [» ]
    2ZXN X-ray 2.10 A 116-423 [» ]
    3A2H X-ray 2.50 A 116-423 [» ]
    3AFR X-ray 2.00 A 116-423 [» ]
    3AUN X-ray 1.81 A 116-423 [» ]
    3VJS X-ray 1.93 A 116-423 [» ]
    3VJT X-ray 2.00 A 116-423 [» ]
    3VRT X-ray 2.40 A 116-423 [» ]
    3VRU X-ray 2.00 A 116-423 [» ]
    3VRV X-ray 1.90 A 116-423 [» ]
    3VRW X-ray 2.40 A 116-423 [» ]
    3VT3 X-ray 1.70 A 116-423 [» ]
    3VT4 X-ray 1.90 A 116-423 [» ]
    3VT5 X-ray 2.11 A 116-423 [» ]
    3VT6 X-ray 2.30 A 116-423 [» ]
    3VT7 X-ray 1.65 A 116-423 [» ]
    3VT8 X-ray 2.10 A 116-423 [» ]
    3VT9 X-ray 2.35 A 116-423 [» ]
    3VTB X-ray 2.00 A 116-423 [» ]
    3VTC X-ray 1.50 A 116-423 [» ]
    3VTD X-ray 2.70 A 116-423 [» ]
    3W0G X-ray 1.94 A 121-420 [» ]
    3W0H X-ray 1.80 A 118-420 [» ]
    3W0I X-ray 1.90 A 121-420 [» ]
    3W0J X-ray 1.84 A 121-420 [» ]
    3W5P X-ray 1.90 A 116-423 [» ]
    3W5Q X-ray 1.90 A 116-423 [» ]
    3W5R X-ray 2.20 A 116-423 [» ]
    3W5T X-ray 2.29 A 116-423 [» ]
    3WT5 X-ray 1.90 A 116-423 [» ]
    3WT6 X-ray 2.00 A 116-423 [» ]
    3WT7 X-ray 2.40 A 116-423 [» ]
    ProteinModelPortali P13053.
    SMRi P13053. Positions 22-106, 118-421.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 246986. 5 interactions.
    MINTi MINT-236433.
    STRINGi 10116.ENSRNOP00000011601.

    Chemistry

    BindingDBi P13053.
    ChEMBLi CHEMBL3150.
    GuidetoPHARMACOLOGYi 605.

    PTM databases

    PhosphoSitei P13053.

    Proteomic databases

    PaxDbi P13053.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 24873.
    KEGGi rno:24873.
    UCSCi RGD:3959. rat.

    Organism-specific databases

    CTDi 7421.
    RGDi 3959. Vdr.

    Phylogenomic databases

    eggNOGi NOG283526.
    HOGENOMi HOG000220844.
    HOVERGENi HBG108655.
    InParanoidi P13053.
    KOi K08539.
    PhylomeDBi P13053.

    Miscellaneous databases

    EvolutionaryTracei P13053.
    NextBioi 604698.
    PROi P13053.

    Gene expression databases

    Genevestigatori P13053.

    Family and domain databases

    Gene3Di 1.10.565.10. 2 hits.
    3.30.50.10. 1 hit.
    InterProi IPR008946. 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 ]
    Pfami PF00104. Hormone_recep. 1 hit.
    PF00105. zf-C4. 1 hit.
    [Graphical view ]
    PRINTSi PR00398. STRDHORMONER.
    PR00047. STROIDFINGER.
    PR00350. VITAMINDR.
    SMARTi SM00430. HOLI. 1 hit.
    SM00399. ZnF_C4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48508. SSF48508. 1 hit.
    PROSITEi PS00031. NUCLEAR_REC_DBD_1. 1 hit.
    PS51030. NUCLEAR_REC_DBD_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiVDR_RAT
    AccessioniPrimary (citable) accession number: P13053
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: October 1, 2014
    This is version 135 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3