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Protein

Vitamin D3 receptor

Gene

Vdr

Organism
Rattus norvegicus (Rat)
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.1 Publication

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

  • calcitriol binding Source: RGD
  • calcitriol receptor activity Source: RGD
  • sequence-specific DNA binding Source: RGD
  • steroid hormone receptor activity Source: InterPro
  • transcription factor activity, sequence-specific DNA binding Source: RGD
  • vitamin D binding Source: RGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • aging Source: RGD
  • apoptotic signaling pathway Source: RGD
  • cellular response to vitamin D Source: RGD
  • heart development Source: RGD
  • regulation of calcium ion transport Source: RGD
  • regulation of transcription from RNA polymerase II promoter Source: RGD
  • response to calcium ion Source: RGD
  • response to estradiol Source: RGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

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
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3959. Vdr.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: RGD
  • dense fibrillar component Source: RGD
  • euchromatin Source: RGD
  • heterochromatin Source: RGD
  • intracellular membrane-bounded organelle Source: RGD
  • nuclear heterochromatin Source: RGD
  • nuclear matrix Source: RGD
  • perinuclear region of cytoplasm Source: RGD
  • T-tubule Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

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.

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 (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 interactors.
MINTiMINT-236433.
STRINGi10116.ENSRNOP00000011601.

Chemistry databases

BindingDBiP13053.

Structurei

Secondary structure

1423
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi116 – 119Combined sources4
Helixi126 – 142Combined sources17
Helixi148 – 152Combined sources5
Turni219 – 222Combined sources4
Helixi223 – 241Combined sources19
Helixi247 – 249Combined sources3
Helixi252 – 270Combined sources19
Helixi271 – 273Combined sources3
Beta strandi274 – 276Combined sources3
Turni277 – 280Combined sources4
Beta strandi281 – 283Combined sources3
Helixi287 – 289Combined sources3
Beta strandi290 – 292Combined sources3
Helixi293 – 297Combined sources5
Turni298 – 300Combined sources3
Helixi303 – 317Combined sources15
Helixi323 – 334Combined sources12
Helixi345 – 366Combined sources22
Turni369 – 374Combined sources6
Helixi375 – 401Combined sources27
Helixi404 – 407Combined sources4
Helixi412 – 418Combined sources7

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[»]
5B5BX-ray2.00A/D116-423[»]
ProteinModelPortaliP13053.
SMRiP13053.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13053.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni90 – 187HingeAdd BLAST98
Regioni188 – 423Ligand-bindingAdd BLAST236
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

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

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

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_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

        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

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.

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[»]
5B5BX-ray2.00A/D116-423[»]
ProteinModelPortaliP13053.
SMRiP13053.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry databases

BindingDBiP13053.
ChEMBLiCHEMBL3150.
GuidetoPHARMACOLOGYi605.

PTM databases

PhosphoSitePlusiP13053.

Proteomic databases

PaxDbiP13053.

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.
PROiP13053.

Family and domain databases

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_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...

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: November 2, 2016
This is version 152 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

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 one 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.