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Q9PTN2

- VDRA_DANRE

UniProt

Q9PTN2 - VDRA_DANRE

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Protein
Vitamin D3 receptor A
Gene
vdra, nr1i1a, vdr
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
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. 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 receptor
Add
BLAST
Zinc fingeri56 – 7621NR C4-type
Add
BLAST
Zinc fingeri92 – 11120NR C4-type
Add
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
Complete GO annotation...

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 A
PRO_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.1 Publication

Protein-protein interaction databases

BioGridi78317. 2 interactions.

Structurei

Secondary structure

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[»]

Miscellaneous databases

EvolutionaryTraceiQ9PTN2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni129 – 21688Hinge
Add
BLAST
Regioni217 – 453237Ligand-binding
Add
BLAST
Regioni255 – 26511Vitamin D3 binding
Add
BLAST
Regioni274 – 29219Interaction with coactivator LXXLL motif
Add
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

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

Sequence conflict

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

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...

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

« 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: April 16, 2014
This is version 90 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

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