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Q9PTN2

- VDRA_DANRE

UniProt

Q9PTN2 - VDRA_DANRE

Protein

Vitamin D3 receptor A

Gene

vdra

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 2 (24 Mar 2009)
      Previous versions | rss
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    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. 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 receptor activity Source: InterPro
    2. ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity Source: ZFIN
    3. sequence-specific DNA binding Source: InterPro
    4. steroid hormone receptor activity Source: InterPro
    5. transcription factor binding Source: ZFIN
    6. vitamin D binding Source: ZFIN
    7. 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

    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

    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 – 17215
    Helixi180 – 1845
    Helixi255 – 27319
    Turni277 – 2815
    Helixi284 – 30219
    Helixi303 – 3053
    Turni309 – 3124
    Beta strandi313 – 3153
    Beta strandi317 – 3193
    Beta strandi321 – 3244
    Helixi325 – 3295
    Turni330 – 3323
    Helixi335 – 34915
    Helixi355 – 36612
    Helixi377 – 39822
    Helixi402 – 4043
    Helixi405 – 43228
    Helixi434 – 4374
    Helixi442 – 4476
    Beta strandi448 – 4503

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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[»]
    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.
    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

    MLTENSAVNS GGKSKCEAGA CESRVNGDAT SVMDLMAVST SATGQDEFDR    50
    NAPRICGVCG DKATGFHFNA MTCEGCKGFF RRSMKRKASF TCPFNGNCTI 100
    TKDNRRHCQA CRLKRCIDIG MMKEFILTDE EVQRKKDLIM KRKEEEAARE 150
    ARKPRLSDEQ MQIINSLVEA HHKTYDDSYS DFVRFRPPVR EGPVTRSASR 200
    AASLHSLSDA SSDSFNHSPE SVDTKLNFSN LLMMYQDSGS PDSSEEDQQS 250
    RLSMLPHLAD LVSYSIQKVI GFAKMIPGFR DLTAEDQIAL LKSSAIEIIM 300
    LRSNQSFSLE DMSWSCGGPD FKYCINDVTK AGHTLELLEP LVKFQVGLKK 350
    LKLHEEEHVL LMAICLLSPD RPGVQDHVRI EALQDRLCDV LQAYIRIQHP 400
    GGRLLYAKMI QKLADLRSLN EEHSKQYRSL SFQPEHSMQL TPLVLEVFGS 450
    EVS 453
    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. 1 PublicationCurated
    Sequence conflicti32 – 321V → L in AAF21427. 1 PublicationCurated
    Sequence conflicti47 – 471E → Q in AAF21427. 1 PublicationCurated
    Sequence conflicti54 – 541R → P in AAF21427. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF164512 mRNA. Translation: AAF21427.1 .
    BC162213 mRNA. Translation: AAI62213.1 .
    BC162226 mRNA. Translation: AAI62226.1 .
    RefSeqi NP_570994.1. NM_130919.1.
    UniGenei Dr.81313.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2HBH X-ray 2.65 A 156-453 [» ]
    2HC4 X-ray 2.20 A 156-453 [» ]
    2HCD X-ray 2.60 A 156-453 [» ]
    3DR1 X-ray 2.70 A 156-453 [» ]
    3O1D X-ray 2.40 A 156-453 [» ]
    3O1E X-ray 2.50 A 156-453 [» ]
    4FHH X-ray 2.33 A 156-453 [» ]
    4FHI X-ray 2.40 A 156-453 [» ]
    4G1D X-ray 2.90 A 156-453 [» ]
    4G1Y X-ray 2.85 A 156-453 [» ]
    4G1Z X-ray 2.50 A 156-453 [» ]
    4G20 X-ray 2.90 A 156-453 [» ]
    4G21 X-ray 2.90 A 156-453 [» ]
    4G2H X-ray 2.50 A 156-453 [» ]
    4IA1 X-ray 2.44 A 156-453 [» ]
    4IA2 X-ray 2.95 A 156-453 [» ]
    4IA3 X-ray 2.70 A 156-453 [» ]
    4IA7 X-ray 2.70 A 156-453 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 78317. 2 interactions.

    Proteomic databases

    PRIDEi Q9PTN2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 30076.
    KEGGi dre:30076.

    Organism-specific databases

    CTDi 30076.
    ZFINi ZDB-GENE-000210-31. vdra.

    Phylogenomic databases

    HOVERGENi HBG108655.
    KOi K08539.
    PhylomeDBi Q9PTN2.

    Miscellaneous databases

    EvolutionaryTracei Q9PTN2.
    NextBioi 20806561.

    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. "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: October 1, 2014
    This is version 91 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