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Protein

Vitamin D3 receptor

Gene

Vdr

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei143 – 1431Vitamin D3By similarity
Binding sitei300 – 3001Vitamin D3By similarity
Binding sitei392 – 3921Vitamin D3By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi21 – 9676Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri24 – 4421NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri60 – 8425NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • bile acid signaling pathway Source: MGI
  • calcium ion transport Source: MGI
  • cell morphogenesis Source: MGI
  • cellular calcium ion homeostasis Source: MGI
  • decidualization Source: Ensembl
  • intestinal absorption Source: MGI
  • lactation Source: MGI
  • mammary gland branching involved in pregnancy Source: MGI
  • multicellular organismal development Source: MGI
  • negative regulation of cell proliferation Source: MGI
  • negative regulation of keratinocyte proliferation Source: MGI
  • negative regulation of transcription, DNA-templated Source: MGI
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • organ morphogenesis Source: MGI
  • positive regulation of apoptotic process involved in mammary gland involution Source: MGI
  • positive regulation of gene expression Source: MGI
  • positive regulation of keratinocyte differentiation Source: MGI
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • positive regulation of vitamin D 24-hydroxylase activity Source: MGI
  • regulation of calcidiol 1-monooxygenase activity Source: BHF-UCL
  • regulation of transcription, DNA-templated Source: MGI
  • skeletal system development Source: MGI
  • vitamin D receptor signaling pathway Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_276696. Nuclear Receptor transcription pathway.

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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:103076. Vdr.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 422422Vitamin D3 receptorPRO_0000053543Add
BLAST

Proteomic databases

MaxQBiP48281.
PRIDEiP48281.

PTM databases

PhosphoSiteiP48281.

Expressioni

Inductioni

By 1,25-dihydroxyvitamin D3 in kidney.1 Publication

Gene expression databases

BgeeiP48281.
CleanExiMM_VDR.
ExpressionAtlasiP48281. baseline and differential.
GenevisibleiP48281. MM.

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

Binary interactionsi

WithEntry#Exp.IntActNotes
Grip1Q925T62EBI-346797,EBI-537752
GTF2BQ004032EBI-346797,EBI-389564From a different organism.
NCOA3Q9Y6Q92EBI-346797,EBI-81196From a different organism.
SNW1Q135732EBI-346797,EBI-632715From a different organism.

Protein-protein interaction databases

BioGridi204511. 4 interactions.
DIPiDIP-31478N.
IntActiP48281. 8 interactions.
STRINGi10090.ENSMUSP00000023119.

Structurei

3D structure databases

ProteinModelPortaliP48281.
SMRiP48281. Positions 22-106, 124-422.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni97 – 18690HingeAdd
BLAST
Regioni187 – 422236Ligand-bindingAdd
BLAST
Regioni222 – 23211Vitamin D3 bindingBy similarityAdd
BLAST
Regioni241 – 25919Interaction with coactivator LXXLL motifBy similarityAdd
BLAST
Regioni266 – 2738Vitamin D3 bindingBy similarity

Domaini

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

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.
GeneTreeiENSGT00780000121834.
HOGENOMiHOG000220844.
HOVERGENiHBG108655.
InParanoidiP48281.
KOiK08539.
OMAiFCQFRPP.
OrthoDBiEOG79KPF8.
TreeFamiTF316304.

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.

P48281-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEAMAASTSL PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR
60 70 80 90 100
SMKRKALFTC PFNGDCRITK DNRRHCQACR LKRCVDIGMM KEFILTDEEV
110 120 130 140 150
QRKREMIMKR KEEEALKDSL RPKLSEEQQH IIAILLDAHH KTYDPTYADF
160 170 180 190 200
RDFRPPIRAD VSTGSYSPRP TLSFSGDSSS NSDLYTPSLD MMEPASFSTM
210 220 230 240 250
DLNEEGSDDP SVTLDLSPLS MLPHLADLVS YSIQKVIGFA KMIPGFRDLT
260 270 280 290 300
SDDQIVLLKS SAIEVIMLRS NQSFTLDDMS WDCGSQDYKY DITDVSRAGH
310 320 330 340 350
TLELIEPLIK FQVGLKKLNL HEEEHVLLMA ICIVSPDRPG VQDAKLVEAI
360 370 380 390 400
QDRLSNTLQT YIRCRHPPPG SHQLYAKMIQ KLADLRSLNE EHSKQYRSLS
410 420
FQPENSMKLT PLVLEVFGNE IS
Length:422
Mass (Da):47,834
Last modified:July 27, 2011 - v2
Checksum:i4614DD4A129F2732
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti276 – 2761L → M in BAA06737 (PubMed:7835717).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31969 mRNA. Translation: BAA06737.1.
AK030339 mRNA. Translation: BAC26911.1.
AK154647 mRNA. Translation: BAE32738.1.
CH466550 Genomic DNA. Translation: EDL04218.1.
BC006716 mRNA. Translation: AAH06716.1.
CCDSiCCDS27784.1.
PIRiPC4019.
RefSeqiNP_033530.2. NM_009504.4.
UniGeneiMm.245084.

Genome annotation databases

EnsembliENSMUST00000023119; ENSMUSP00000023119; ENSMUSG00000022479.
GeneIDi22337.
KEGGimmu:22337.
UCSCiuc007xlk.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31969 mRNA. Translation: BAA06737.1.
AK030339 mRNA. Translation: BAC26911.1.
AK154647 mRNA. Translation: BAE32738.1.
CH466550 Genomic DNA. Translation: EDL04218.1.
BC006716 mRNA. Translation: AAH06716.1.
CCDSiCCDS27784.1.
PIRiPC4019.
RefSeqiNP_033530.2. NM_009504.4.
UniGeneiMm.245084.

3D structure databases

ProteinModelPortaliP48281.
SMRiP48281. Positions 22-106, 124-422.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204511. 4 interactions.
DIPiDIP-31478N.
IntActiP48281. 8 interactions.
STRINGi10090.ENSMUSP00000023119.

Chemistry

BindingDBiP48281.
ChEMBLiCHEMBL5601.
GuidetoPHARMACOLOGYi605.

PTM databases

PhosphoSiteiP48281.

Proteomic databases

MaxQBiP48281.
PRIDEiP48281.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000023119; ENSMUSP00000023119; ENSMUSG00000022479.
GeneIDi22337.
KEGGimmu:22337.
UCSCiuc007xlk.1. mouse.

Organism-specific databases

CTDi7421.
MGIiMGI:103076. Vdr.

Phylogenomic databases

eggNOGiNOG283526.
GeneTreeiENSGT00780000121834.
HOGENOMiHOG000220844.
HOVERGENiHBG108655.
InParanoidiP48281.
KOiK08539.
OMAiFCQFRPP.
OrthoDBiEOG79KPF8.
TreeFamiTF316304.

Enzyme and pathway databases

ReactomeiREACT_276696. Nuclear Receptor transcription pathway.

Miscellaneous databases

ChiTaRSiVdr. mouse.
NextBioi302589.
PROiP48281.
SOURCEiSearch...

Gene expression databases

BgeeiP48281.
CleanExiMM_VDR.
ExpressionAtlasiP48281. baseline and differential.
GenevisibleiP48281. MM.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the gene encoding the mouse vitamin D receptor."
    Kamei Y., Kawada T., Fukuwatari T., Ono T., Kato S., Sugimoto E.
    Gene 152:281-282(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J and NOD.
    Tissue: Intestine.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Mammary tumor.
  5. "Klotho, a gene related to a syndrome resembling human premature aging, functions in a negative regulatory circuit of vitamin D endocrine system."
    Tsujikawa H., Kurotaki Y., Fujimori T., Fukuda K., Nabeshima Y.
    Mol. Endocrinol. 17:2393-2403(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.

Entry informationi

Entry nameiVDR_MOUSE
AccessioniPrimary (citable) accession number: P48281
Secondary accession number(s): Q922X0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: July 27, 2011
Last modified: June 24, 2015
This is version 134 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.