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Protein

Vitamin D3 receptor A

Gene

vdra

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
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 sitei175Vitamin D31
Binding sitei333Vitamin D31
Binding sitei423Vitamin D31

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi53 – 128Nuclear receptorPROSITE-ProRule annotationAdd BLAST76
Zinc fingeri56 – 76NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri92 – 111NR C4-typePROSITE-ProRule annotationAdd BLAST20

GO - Molecular functioni

  • calcitriol binding Source: ZFIN
  • calcitriol receptor activity Source: ZFIN
  • lithocholic acid binding Source: ZFIN
  • nuclear receptor activity Source: ZFIN
  • sequence-specific DNA binding Source: InterPro
  • steroid hormone receptor activity Source: InterPro
  • transcription factor binding Source: ZFIN
  • vitamin D binding Source: ZFIN
  • zinc ion binding Source: InterPro

GO - Biological processi

  • calcium ion homeostasis Source: ZFIN
  • heart jogging Source: ZFIN
  • heart looping Source: ZFIN
  • hematopoietic stem cell proliferation Source: ZFIN
  • ossification Source: ZFIN
  • regulation of transcription, DNA-templated Source: ZFIN
  • transcription, DNA-templated Source: ZFIN

Keywordsi

Molecular functionDNA-binding, Receptor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Vitamin D3 receptor A
Short name:
VDR-A
Alternative name(s):
1,25-dihydroxyvitamin D3 receptor A
Nuclear receptor subfamily 1 group I member 1-A
Gene namesi
Name:vdra
Synonyms:nr1i1a, vdr
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-000210-31 vdra

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

ChEMBLiCHEMBL3217399

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003378781 – 453Vitamin D3 receptor AAdd BLAST453

Proteomic databases

PRIDEiQ9PTN2

Expressioni

Tissue specificityi

Detected in embryo 24 to 48 hours after fertilization and in gastrula.1 Publication

Interactioni

Subunit structurei

Homodimer in the absence of bound vitamin D3. Heterodimer with RXRA after vitamin D3 binding (By similarity). Interacts with ncoa1 and possibly other coactivators, leading to a strong increase of transcription of target genes (PubMed:17218092, PubMed:17346665).By similarity2 Publications

GO - Molecular functioni

  • transcription factor binding Source: ZFIN

Protein-protein interaction databases

BioGridi783172 interactors.

Structurei

Secondary structure

1453
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi158 – 174Combined sources17
Helixi180 – 184Combined sources5
Helixi255 – 274Combined sources20
Turni277 – 281Combined sources5
Helixi284 – 302Combined sources19
Helixi303 – 305Combined sources3
Turni309 – 312Combined sources4
Beta strandi313 – 315Combined sources3
Helixi319 – 321Combined sources3
Beta strandi322 – 324Combined sources3
Helixi325 – 328Combined sources4
Turni329 – 331Combined sources3
Helixi335 – 349Combined sources15
Helixi355 – 366Combined sources12
Helixi377 – 398Combined sources22
Helixi402 – 404Combined sources3
Helixi405 – 431Combined sources27
Helixi434 – 437Combined sources4
Helixi442 – 448Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HBHX-ray2.65A156-453[»]
2HC4X-ray2.20A156-453[»]
2HCDX-ray2.60A156-453[»]
3DR1X-ray2.70A156-453[»]
3O1DX-ray2.40A156-453[»]
3O1EX-ray2.50A156-453[»]
4FHHX-ray2.33A156-453[»]
4FHIX-ray2.40A156-453[»]
4G1DX-ray2.90A156-453[»]
4G1YX-ray2.85A156-453[»]
4G1ZX-ray2.50A156-453[»]
4G20X-ray2.90A156-453[»]
4G21X-ray2.90A156-453[»]
4G2HX-ray2.50A156-453[»]
4IA1X-ray2.44A156-453[»]
4IA2X-ray2.95A156-453[»]
4IA3X-ray2.70A156-453[»]
4IA7X-ray2.70A156-453[»]
4Q0AX-ray1.90C156-453[»]
4RUJX-ray2.35A156-453[»]
4RUOX-ray2.81X156-453[»]
4RUPX-ray2.75A156-453[»]
5E7VX-ray2.40A156-453[»]
5LGAX-ray2.50A156-453[»]
5MX7X-ray1.98A1156-453[»]
5NKYX-ray2.10A156-453[»]
5NMAX-ray2.80A156-453[»]
5NMBX-ray2.50A2156-453[»]
5OW7X-ray2.10A156-453[»]
5OW9X-ray2.40A156-453[»]
5OWDX-ray2.15A156-453[»]
SMRiQ9PTN2
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9PTN2

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini159 – 449NR LBDPROSITE-ProRule annotationAdd BLAST291

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni129 – 158HingeAdd BLAST30
Regioni255 – 265Vitamin D3 bindingAdd BLAST11
Regioni274 – 292Interaction with coactivator LXXLL motifAdd BLAST19
Regioni299 – 306Vitamin 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 fingeri56 – 76NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri92 – 111NR C4-typePROSITE-ProRule annotationAdd BLAST20

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOVERGENiHBG108655
InParanoidiQ9PTN2
KOiK08539
PhylomeDBiQ9PTN2

Family and domain databases

Gene3Di3.30.50.101 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

Sequencei

Sequence statusi: Complete.

Q9PTN2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLTENSAVNS GGKSKCEAGA CESRVNGDAT SVMDLMAVST SATGQDEFDR
60 70 80 90 100
NAPRICGVCG DKATGFHFNA MTCEGCKGFF RRSMKRKASF TCPFNGNCTI
110 120 130 140 150
TKDNRRHCQA CRLKRCIDIG MMKEFILTDE EVQRKKDLIM KRKEEEAARE
160 170 180 190 200
ARKPRLSDEQ MQIINSLVEA HHKTYDDSYS DFVRFRPPVR EGPVTRSASR
210 220 230 240 250
AASLHSLSDA SSDSFNHSPE SVDTKLNFSN LLMMYQDSGS PDSSEEDQQS
260 270 280 290 300
RLSMLPHLAD LVSYSIQKVI GFAKMIPGFR DLTAEDQIAL LKSSAIEIIM
310 320 330 340 350
LRSNQSFSLE DMSWSCGGPD FKYCINDVTK AGHTLELLEP LVKFQVGLKK
360 370 380 390 400
LKLHEEEHVL LMAICLLSPD RPGVQDHVRI EALQDRLCDV LQAYIRIQHP
410 420 430 440 450
GGRLLYAKMI QKLADLRSLN EEHSKQYRSL SFQPEHSMQL TPLVLEVFGS

EVS
Length:453
Mass (Da):50,867
Last modified:March 24, 2009 - v2
Checksum:i87DE0415B3FF56CD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti24R → T in AAF21427 (Ref. 1) Curated1
Sequence conflicti32V → L in AAF21427 (Ref. 1) Curated1
Sequence conflicti47E → Q in AAF21427 (Ref. 1) Curated1
Sequence conflicti54R → P in AAF21427 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF164512 mRNA Translation: AAF21427.1
BC162213 mRNA Translation: AAI62213.1
BC162226 mRNA Translation: AAI62226.1
RefSeqiNP_570994.1, NM_130919.1
UniGeneiDr.81313

Genome annotation databases

GeneIDi30076
KEGGidre:30076

Similar proteinsi

Entry informationi

Entry nameiVDRA_DANRE
AccessioniPrimary (citable) accession number: Q9PTN2
Secondary accession number(s): B3DFZ0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: March 24, 2009
Last modified: March 28, 2018
This is version 118 of the entry and version 2 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