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- PDB-3dr1: Side-chain fluorine atoms of non-steroidal vitamin D3 analogs sta... -

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Basic information

Entry
Database: PDB / ID: 3dr1
TitleSide-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix 12 of vitamin D receptor
Components
  • SRC-1 (LXXLL motif) from Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsGENE REGULATION/TRANSFERASE / GENE REGULATION / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription / Transcription regulation / Zinc / Zinc-finger / Activator / Acyltransferase / Alternative splicing / Chromosomal rearrangement / Phosphoprotein / Polymorphism / Proto-oncogene / Transferase / Ubl conjugation / GENE REGULATION-TRANSFERASE COMPLEX
Function / homology
Function and homology information


Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Recycling of bile acids and salts / BMAL1:CLOCK,NPAS2 activates circadian gene expression / RORA activates gene expression / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / PPARA activates gene expression / SUMOylation of transcription cofactors / Circadian Clock / Estrogen-dependent gene expression ...Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Recycling of bile acids and salts / BMAL1:CLOCK,NPAS2 activates circadian gene expression / RORA activates gene expression / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / PPARA activates gene expression / SUMOylation of transcription cofactors / Circadian Clock / Estrogen-dependent gene expression / Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) / Transcriptional regulation of white adipocyte differentiation / HATs acetylate histones / Activation of gene expression by SREBF (SREBP) / Transcriptional activation of mitochondrial biogenesis / Endogenous sterols / heart jogging / hematopoietic stem cell proliferation / lithocholic acid binding / calcitriol binding / calcium ion homeostasis / vitamin D binding / labyrinthine layer morphogenesis / regulation of cellular response to drug / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone mediated signaling pathway / progesterone receptor binding / male mating behavior / positive regulation of female receptivity / heart looping / hypothalamus development / RNA polymerase II regulatory region DNA binding / histone H4 acetylation / estrous cycle / cellular response to Thyroglobulin triiodothyronine / bile acid and bile salt transport / histone acetyltransferase / histone acetyltransferase activity / retinoid X receptor binding / aryl hydrocarbon receptor binding / androgen receptor signaling pathway / ossification / cerebellum development / cellular response to hormone stimulus / androgen receptor binding / positive regulation of neuron differentiation / nuclear receptor binding / cerebral cortex development / nuclear hormone receptor binding / lactation / response to retinoic acid / hippocampus development / response to progesterone / RNA polymerase II transcription factor complex / estrogen receptor binding / steroid hormone receptor activity / transcription regulatory region sequence-specific DNA binding / regulation of lipid metabolic process / nuclear receptor transcription coactivator activity / male gonad development / RNA polymerase II regulatory region sequence-specific DNA binding / nuclear receptor activity / protein N-terminus binding / response to estradiol / signaling receptor activity / transcription coactivator activity / multicellular organism development / nuclear chromatin / protein dimerization activity / transcription, DNA-templated / cell differentiation / protein-containing complex binding / neuron projection / positive regulation of apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription factor binding / chromatin binding / regulation of transcription, DNA-templated / positive regulation of transcription, DNA-templated / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Nuclear hormones receptors DNA-binding region signature. / Nuclear receptor coactivator, interlocking / Nuclear hormone receptor-like domain superfamily / Nuclear receptor coactivator 1 / Nuclear receptor coactivator / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator, Ncoa-type, interlocking / PAS fold / Zinc finger, NHR/GATA-type / Myc-type, basic helix-loop-helix (bHLH) domain ...Nuclear hormones receptors DNA-binding region signature. / Nuclear receptor coactivator, interlocking / Nuclear hormone receptor-like domain superfamily / Nuclear receptor coactivator 1 / Nuclear receptor coactivator / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator, Ncoa-type, interlocking / PAS fold / Zinc finger, NHR/GATA-type / Myc-type, basic helix-loop-helix (bHLH) domain / Domain of unknown function DUF1518 / Nuclear hormone receptor / Zinc finger, nuclear hormone receptor-type / Nuclear hormone receptor, ligand-binding domain / Vitamin D receptor / PAS repeat profile. / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / PAS domain / Nuclear hormone receptors DNA-binding domain profile. / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS domain superfamily / Zinc finger, C4 type (two domains) / Ligand-binding domain of nuclear hormone receptor / Helix-loop-helix DNA-binding domain / VDR, DNA-binding domain / PAS fold / Domain of unknown function (DUF1518) / Nuclear receptor coactivator / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Steroid receptor coactivator / Helix-loop-helix DNA-binding domain superfamily
Nuclear receptor coactivator 1 / Vitamin D3 receptor A
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSato, Y. / Rochel, N. / Moras, D.
CitationJournal: Chem.Biol. / Year: 2008
Title: Superagonistic fluorinated vitamin D3 analogs stabilize helix 12 of the vitamin D receptor.
Authors: Eelen, G. / Valle, N. / Sato, Y. / Rochel, N. / Verlinden, L. / De Clercq, P. / Moras, D. / Bouillon, R. / Munoz, A. / Verstuyf, A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor A
B: SRC-1 (LXXLL motif) from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3444
Polymers35,8372
Non-polymers5072
Water1,11762
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)66.100, 66.100, 265.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein/peptide Vitamin D3 receptor A / VDR-A / 1 / 25-dihydroxyvitamin D3 receptor A / Nuclear receptor subfamily 1 group I member 1-A


Mass: 34060.672 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21de3 / References: UniProt: Q9PTN2
#2: Protein/peptide SRC-1 (LXXLL motif) from Nuclear receptor coactivator 1 / NCoA-1 / Steroid receptor coactivator 1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52


Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human)
References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Chemical ChemComp-C5D / (1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol


Mass: 482.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32F6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Li sulfate 1.6M, Mg sulfate 50mM, Bis Tris 0.1M , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2007
RadiationMonochromator: Si(311) or Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10290 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 13.4 % / Biso Wilson estimate: 56.8 Å2 / Rsym value: 0.111 / Net I/σ(I): 30.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 13.4 / Num. unique all: 990 / Rsym value: 0.299 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HC4
Resolution: 2.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.286 541 -RANDOM
Rwork0.226 ---
Obs-10242 99.9 %-
Displacement parametersBiso mean: 48.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 34 62 2119
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.106
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.305 53 -
Rwork0.264 --
Obs-937 100 %

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