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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)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
  • RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding 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
  • ossification Source: ZFIN
  • regulation of transcription, DNA-templated Source: ZFIN
  • 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
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-000210-31. vdra.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

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

GO - Molecular functioni

  • transcription factor binding Source: ZFIN

Protein-protein interaction databases

BioGridi78317. 2 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[»]
SMRiQ9PTN2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9PTN2.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni129 – 216HingeAdd BLAST88
Regioni217 – 453Ligand-bindingAdd BLAST237
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

Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

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

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_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)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.

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
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[»]
SMRiQ9PTN2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi78317. 2 interactors.

Chemistry databases

ChEMBLiCHEMBL3217399.

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.
PROiQ9PTN2.

Family and domain databases

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_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...

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: November 30, 2016
This is version 108 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

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 one 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.