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P13053

- VDR_RAT

UniProt

P13053 - VDR_RAT

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Protein

Vitamin D3 receptor

Gene

Vdr

Organism
Rattus norvegicus (Rat)
Status
Reviewed - 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. 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. sequence-specific DNA binding Source: RGD
  4. sequence-specific DNA binding transcription factor activity Source: RGD
  5. steroid hormone receptor activity Source: InterPro
  6. vitamin D binding Source: RGD
  7. 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
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
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
Complete GO annotation...

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 [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:
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 29, 2014
This is version 136 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