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Q9PTN2 (VDRA_DANRE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:vdra
Synonyms:nr1i1a, vdr
OrganismDanio rerio (Zebrafish) (Brachydanio rerio) [Reference proteome]
Taxonomic identifier7955 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio

Protein attributes

Sequence length453 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5

Subunit structure

Interacts with ncoa1 and possibly other coactivators, leading to a strong increase of transcription of target genes. Ref.5

Subcellular location

Nucleus.

Tissue specificity

Detected in embryo 24 to 48 hours after fertilization and in gastrula. Ref.3

Domain

Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionReceptor
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcalcium ion homeostasis

Inferred from mutant phenotype PubMed 23029160. Source: ZFIN

intracellular receptor signaling pathway

Inferred from direct assay PubMed 17997857. Source: GOC

ossification

Inferred from mutant phenotype PubMed 23029160. Source: ZFIN

regulation of transcription, DNA-templated

Inferred from direct assay PubMed 17997857. Source: ZFIN

transcription, DNA-templated

Inferred from direct assay PubMed 17997857. Source: ZFIN

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncalcitriol receptor activity

Inferred from electronic annotation. Source: InterPro

ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity

Inferred from direct assay PubMed 17997857. Source: ZFIN

sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

steroid hormone receptor activity

Inferred from electronic annotation. Source: InterPro

transcription factor binding

Inferred from physical interaction PubMed 20236534. Source: ZFIN

vitamin D binding

Inferred from direct assay PubMed 15225747. Source: ZFIN

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 453453Vitamin D3 receptor A
PRO_0000337878

Regions

DNA binding53 – 12876Nuclear receptor
Zinc finger56 – 7621NR C4-type
Zinc finger92 – 11120NR C4-type
Region129 – 21688Hinge
Region217 – 453237Ligand-binding
Region255 – 26511Vitamin D3 binding
Region274 – 29219Interaction with coactivator LXXLL motif
Region299 – 3068Vitamin D3 binding

Sites

Binding site1751Vitamin D3
Binding site3331Vitamin D3
Binding site4231Vitamin D3

Experimental info

Sequence conflict241R → T in AAF21427. Ref.1
Sequence conflict321V → L in AAF21427. Ref.1
Sequence conflict471E → Q in AAF21427. Ref.1
Sequence conflict541R → P in AAF21427. Ref.1

Secondary structure

................................... 453
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9PTN2 [UniParc].

Last modified March 24, 2009. Version 2.
Checksum: 87DE0415B3FF56CD

FASTA45350,867
        10         20         30         40         50         60 
MLTENSAVNS GGKSKCEAGA CESRVNGDAT SVMDLMAVST SATGQDEFDR NAPRICGVCG 

        70         80         90        100        110        120 
DKATGFHFNA MTCEGCKGFF RRSMKRKASF TCPFNGNCTI TKDNRRHCQA CRLKRCIDIG 

       130        140        150        160        170        180 
MMKEFILTDE EVQRKKDLIM KRKEEEAARE ARKPRLSDEQ MQIINSLVEA HHKTYDDSYS 

       190        200        210        220        230        240 
DFVRFRPPVR EGPVTRSASR AASLHSLSDA SSDSFNHSPE SVDTKLNFSN LLMMYQDSGS 

       250        260        270        280        290        300 
PDSSEEDQQS RLSMLPHLAD LVSYSIQKVI GFAKMIPGFR DLTAEDQIAL LKSSAIEIIM 

       310        320        330        340        350        360 
LRSNQSFSLE DMSWSCGGPD FKYCINDVTK AGHTLELLEP LVKFQVGLKK LKLHEEEHVL 

       370        380        390        400        410        420 
LMAICLLSPD RPGVQDHVRI EALQDRLCDV LQAYIRIQHP GGRLLYAKMI QKLADLRSLN 

       430        440        450 
EEHSKQYRSL SFQPEHSMQL TPLVLEVFGS EVS 

« Hide

References

« Hide 'large scale' references
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF164512 mRNA. Translation: AAF21427.1.
BC162213 mRNA. Translation: AAI62213.1.
BC162226 mRNA. Translation: AAI62226.1.
RefSeqNP_570994.1. NM_130919.1.
UniGeneDr.81313.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid78317. 2 interactions.

Proteomic databases

PRIDEQ9PTN2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID30076.
KEGGdre:30076.

Organism-specific databases

CTD30076.
ZFINZDB-GENE-000210-31. vdra.

Phylogenomic databases

HOVERGENHBG108655.
KOK08539.
PhylomeDBQ9PTN2.

Family and domain databases

Gene3D1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProIPR008946. 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]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR00398. STRDHORMONER.
PR00047. STROIDFINGER.
PR00350. VITAMINDR.
SMARTSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMSSF48508. SSF48508. 1 hit.
PROSITEPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9PTN2.
NextBio20806561.

Entry information

Entry nameVDRA_DANRE
AccessionPrimary (citable) accession number: Q9PTN2
Secondary accession number(s): B3DFZ0
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references