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Protein

Vitamin D3 receptor

Gene

Vdr

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells. Enters the nucleus upon vitamin D3 binding where it forms heterodimers with the retinoid X receptor/RXR. The VDR-RXR heterodimers bind to specific response elements on DNA and activate the transcription of vitamin D3-responsive target 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)DescriptionActionsGraphical viewLength
Binding sitei143Vitamin D31
Binding sitei301Vitamin D31
Binding sitei393Vitamin D31

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi24 – 89Nuclear receptorPROSITE-ProRule annotationAdd BLAST66
Zinc fingeri24 – 44NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri60 – 84NR C4-typePROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Receptor
Biological processTranscription, Transcription regulation
LigandMetal-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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3959 Vdr

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL3150
GuidetoPHARMACOLOGYi605

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000535441 – 423Vitamin D3 receptorAdd BLAST423

Proteomic databases

PaxDbiP13053
PRIDEiP13053

PTM databases

PhosphoSitePlusiP13053

Expressioni

Tissue specificityi

Detected in intestine and kidney.1 Publication

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 with the corepressor NCOR1. 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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi246986, 5 interactors
MINTiP13053
STRINGi10116.ENSRNOP00000011601

Chemistry databases

BindingDBiP13053

Structurei

Secondary structure

1423
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP13053
SMRiP13053
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13053

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini127 – 419NR LBDPROSITE-ProRule annotationAdd BLAST293

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni90 – 126HingeAdd BLAST37
Regioni223 – 233Vitamin D3 bindingAdd BLAST11
Regioni242 – 260Interaction with coactivator LXXLL motifAdd BLAST19
Regioni267 – 274Vitamin D3 binding8

Domaini

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

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri24 – 44NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri60 – 84NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575 Eukaryota
ENOG410XRZC LUCA
HOGENOMiHOG000220844
HOVERGENiHBG108655
InParanoidiP13053
KOiK08539
PhylomeDBiP13053

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR000324 VitD_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR00398 STRDHORMONER
PR00047 STROIDFINGER
PR00350 VITAMINDR
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

P13053-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEATAASTSL 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
RDFRPPVRMD GSTGSYSPRP TLSFSGNSSS SSSDLYTTSL DMMEPSGFSN
210 220 230 240 250
LDLNGEDSDD PSVTLDLSPL SMLPHLADLV SYSIQKVIGF AKMIPGFRDL
260 270 280 290 300
TSDDQIVLLK SSAIEVIMLR SNQSFTMDDM SWDCGSQDYK YDVTDVSKAG
310 320 330 340 350
HTLELIEPLI KFQVGLKKLN LHEEEHVLLM AICIVSPDRP GVQDAKLVEA
360 370 380 390 400
IQDRLSNTLQ TYIRCRHPPP GSHQLYAKMI QKLADLRSLN EEHSKQYRSL
410 420
SFQPENSMKL TPLVLEVFGN EIS
Length:423
Mass (Da):47,814
Last modified:January 1, 1990 - v1
Checksum:i1A0E519A9DCCE990
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
G3V744G3V744_RAT
Vitamin D receptor
Vdr rCG_50856
423Annotation score:

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04147 mRNA Translation: AAA41089.1
PIRiA31761
RefSeqiNP_058754.1, NM_017058.1
UniGeneiRn.10911

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
3WTQX-ray2.10A116-423[»]
4YNKX-ray2.30A116-423[»]
5AWJX-ray2.20A116-423[»]
5AWKX-ray2.90A116-423[»]
5B41X-ray1.89A116-423[»]
5B5BX-ray2.00A/D116-423[»]
5GICX-ray2.35A124-420[»]
5GIDX-ray2.15A124-419[»]
5GIEX-ray2.39A/D117-419[»]
5H1EX-ray2.60A116-423[»]
5XPLX-ray2.05A116-423[»]
5XPMX-ray2.20A116-423[»]
5XPNX-ray1.96A116-423[»]
5XPOX-ray2.28A116-423[»]
5XPPX-ray2.85A116-423[»]
5XUQX-ray2.80A116-423[»]
5XZFX-ray2.10A116-423[»]
5XZHX-ray2.00A116-423[»]
5ZWEX-ray2.72A116-423[»]
5ZWFX-ray2.10A116-423[»]
5ZWHX-ray2.38A116-423[»]
5ZWIX-ray2.40A116-423[»]
ProteinModelPortaliP13053
SMRiP13053
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi246986, 5 interactors
MINTiP13053
STRINGi10116.ENSRNOP00000011601

Chemistry databases

BindingDBiP13053
ChEMBLiCHEMBL3150
GuidetoPHARMACOLOGYi605

PTM databases

PhosphoSitePlusiP13053

Proteomic databases

PaxDbiP13053
PRIDEiP13053

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi24873
KEGGirno:24873
UCSCiRGD:3959 rat

Organism-specific databases

CTDi7421
RGDi3959 Vdr

Phylogenomic databases

eggNOGiKOG3575 Eukaryota
ENOG410XRZC LUCA
HOGENOMiHOG000220844
HOVERGENiHBG108655
InParanoidiP13053
KOiK08539
PhylomeDBiP13053

Miscellaneous databases

EvolutionaryTraceiP13053
PROiPR:P13053

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR000324 VitD_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR00398 STRDHORMONER
PR00047 STROIDFINGER
PR00350 VITAMINDR
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiVDR_RAT
AccessioniPrimary (citable) accession number: P13053
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: November 7, 2018
This is version 168 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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