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Basic information

Entry
Database: PDB / ID: 3ogt
TitleDesign, Chemical synthesis, Functional characterization and Crystal structure of the sidechain analogue of 1,25-dihydroxyvitamin D3.
ComponentsVitamin D3 receptor
KeywordsTRANSCRIPTION / Transcription factor / Vitamin D / nucleus
Function / homology
Function and homology information


regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / response to bile acid / nuclear receptor-mediated bile acid signaling pathway / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / response to bile acid / nuclear receptor-mediated bile acid signaling pathway / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / Nuclear Receptor transcription pathway / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / calcium ion transport / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. ...Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FMV / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsHuet, T. / Fraga, R. / Mourino, A. / Moras, D. / Rochel, N.
CitationJournal: To be Published
Title: Design, Chemical synthesis, Functional characterization and Crystal structure of the sidechain analogue of 1,25-dihydroxyvitamin D3.
Authors: Huet, T. / Fraga, R. / Mourino, A. / Moras, D. / Rochel, N.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin D3 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0254
Polymers29,3921
Non-polymers6333
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.018, 51.622, 132.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29391.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDR, NR1I1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P11473
#2: Chemical ChemComp-FMV / (1S,3R,5Z,7E,14beta,17alpha,20S)-20-[5-(1-hydroxy-1-methylethyl)furan-2-yl]-9,10-secopregna-5,7,10-triene-1,3-diol


Mass: 440.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH6.0, 1.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2009
RadiationMonochromator: Horizontally diffracting monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 32327 / Num. obs: 32016 / % possible obs: 99.1 % / Observed criterion σ(I): 14.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→23.731 Å / SU ML: 0.16 / σ(F): 1.34 / σ(I): 3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 1606 5.05 %RANDOM
Rwork0.1598 ---
obs0.161 31771 99.08 %-
all-32327 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.015 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0291 Å20 Å20 Å2
2--0.6828 Å20 Å2
3---0.3464 Å2
Refinement stepCycle: LAST / Resolution: 1.75→23.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 42 365 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072162
X-RAY DIFFRACTIONf_angle_d1.5022955
X-RAY DIFFRACTIONf_dihedral_angle_d15.316849
X-RAY DIFFRACTIONf_chiral_restr0.077343
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.21911500.18862728X-RAY DIFFRACTION100
1.8065-1.8710.20831530.18212709X-RAY DIFFRACTION100
1.871-1.94590.21261490.16412702X-RAY DIFFRACTION100
1.9459-2.03440.17511410.15092740X-RAY DIFFRACTION100
2.0344-2.14160.17651400.13622738X-RAY DIFFRACTION100
2.1416-2.27570.16521290.13882743X-RAY DIFFRACTION100
2.2757-2.45120.1651360.15292772X-RAY DIFFRACTION100
2.4512-2.69760.19421550.16312714X-RAY DIFFRACTION99
2.6976-3.08720.18981640.16922729X-RAY DIFFRACTION99
3.0872-3.88680.17811400.14472764X-RAY DIFFRACTION98
3.8868-23.73320.16861490.16382826X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 13.5598 Å / Origin y: 20.3841 Å / Origin z: 42.0445 Å
111213212223313233
T0.0074 Å2-0.0062 Å2-0.0067 Å2-0.0017 Å2-0.008 Å2--0.0121 Å2
L0.7118 °2-0.118 °20.249 °2-0.6202 °20.0147 °2--0.8884 °2
S-0.0081 Å °-0.0317 Å °0.072 Å °0.0479 Å °-0.0019 Å °-0.0213 Å °-0.0069 Å °0.0163 Å °0.0113 Å °
Refinement TLS groupSelection details: all

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