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Protein

Vitamin D3 receptor A

Gene

vdra

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
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. Plays a central role in calcium homeostasis.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei175 – 1751Vitamin D3
Binding sitei333 – 3331Vitamin D3
Binding sitei423 – 4231Vitamin D3

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi53 – 12876Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri56 – 7621NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri92 – 11120NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. calcitriol binding Source: ZFIN
  2. calcitriol receptor activity Source: InterPro
  3. ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity Source: ZFIN
  4. lithocholic acid binding Source: ZFIN
  5. sequence-specific DNA binding Source: InterPro
  6. steroid hormone receptor activity Source: InterPro
  7. transcription factor binding Source: ZFIN
  8. vitamin D binding Source: ZFIN
  9. zinc ion binding Source: InterPro

GO - Biological processi

  1. calcium ion homeostasis Source: ZFIN
  2. intracellular receptor signaling pathway Source: GOC
  3. ossification Source: ZFIN
  4. regulation of transcription, DNA-templated Source: ZFIN
  5. transcription, DNA-templated Source: ZFIN
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 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
ProteomesiUP000000437: Unplaced

Organism-specific databases

ZFINiZDB-GENE-000210-31. vdra.

Subcellular locationi

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 453453Vitamin D3 receptor APRO_0000337878Add
BLAST

Proteomic databases

PRIDEiQ9PTN2.

Expressioni

Tissue specificityi

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

Interactioni

Subunit structurei

Interacts with ncoa1 and possibly other coactivators, leading to a strong increase of transcription of target genes.2 Publications

Protein-protein interaction databases

BioGridi78317. 2 interactions.

Structurei

Secondary structure

1
453
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi158 – 17417Combined sources
Helixi180 – 1845Combined sources
Helixi255 – 27420Combined sources
Turni277 – 2815Combined sources
Helixi284 – 30219Combined sources
Helixi303 – 3053Combined sources
Turni309 – 3124Combined sources
Beta strandi313 – 3153Combined sources
Helixi319 – 3213Combined sources
Beta strandi322 – 3243Combined sources
Helixi325 – 3284Combined sources
Turni329 – 3313Combined sources
Helixi335 – 34915Combined sources
Helixi355 – 36612Combined sources
Helixi377 – 39822Combined sources
Helixi402 – 4043Combined sources
Helixi405 – 43127Combined sources
Helixi434 – 4374Combined sources
Helixi442 – 4487Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9PTN2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni129 – 21688HingeAdd
BLAST
Regioni217 – 453237Ligand-bindingAdd
BLAST
Regioni255 – 26511Vitamin D3 bindingAdd
BLAST
Regioni274 – 29219Interaction with coactivator LXXLL motifAdd
BLAST
Regioni299 – 3068Vitamin 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 fingeri56 – 7621NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri92 – 11120NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOVERGENiHBG108655.
InParanoidiQ9PTN2.
KOiK08539.
PhylomeDBiQ9PTN2.

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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti24 – 241R → T in AAF21427 (Ref. 1) Curated
Sequence conflicti32 – 321V → L in AAF21427 (Ref. 1) Curated
Sequence conflicti47 – 471E → Q in AAF21427 (Ref. 1) Curated
Sequence conflicti54 – 541R → P in AAF21427 (Ref. 1) Curated

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.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi78317. 2 interactions.

Proteomic databases

PRIDEiQ9PTN2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi30076.
KEGGidre:30076.

Organism-specific databases

CTDi30076.
ZFINiZDB-GENE-000210-31. vdra.

Phylogenomic databases

HOVERGENiHBG108655.
InParanoidiQ9PTN2.
KOiK08539.
PhylomeDBiQ9PTN2.

Miscellaneous databases

EvolutionaryTraceiQ9PTN2.
NextBioi20806561.

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. "Danio rerio vitamin D receptor."
    Kouzmenko A.P.
    Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression."
    Bertrand S., Thisse B., Tavares R., Sachs L., Chaumot A., Bardet P.-L., Escriva H., Duffraisse M., Marchand O., Safi R., Thisse C., Laudet V.
    PLoS Genet. 3:E188-E188(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  4. "Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol."
    Rochel N., Hourai S., Perez-Garcia X., Rumbo A., Mourino A., Moras D.
    Arch. Biochem. Biophys. 460:172-176(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 156-453 IN COMPLEX WITH VITAMIN D3 ANALOG AND NCOA1, IDENTIFICATION BY MASS SPECTROMETRY.
  5. "Adaptability of the vitamin D nuclear receptor to the synthetic ligand Gemini: remodelling the LBP with one side chain rotation."
    Ciesielski F., Rochel N., Moras D.
    J. Steroid Biochem. Mol. Biol. 103:235-242(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 156-453 IN COMPLEXES WITH VITAMIN D3; LIGAND ANALOG AND NCOA1, FUNCTION, INTERACTION WITH NCOA1, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiVDRA_DANRE
AccessioniPrimary (citable) accession number: Q9PTN2
Secondary accession number(s): B3DFZ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: March 24, 2009
Last modified: March 4, 2015
This is version 95 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

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

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.