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- PDB-2har: Crystal structure of VDR LBD in complex with 2 alpha-(3-hydroxy-1... -

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Basic information

Entry
Database: PDB / ID: 2har
TitleCrystal structure of VDR LBD in complex with 2 alpha-(3-hydroxy-1-propoxy) calcitriol
ComponentsVitamin D3 receptor
KeywordsGENE REGULATION / alpha helical sandwich
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 / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / retinoic acid receptor signaling pathway / 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-OCC / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHourai, S. / Rochel, N. / Moras, D.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Probing a Water Channel near the A-Ring of Receptor-Bound 1alpha,25-Dihydroxyvitamin D3 with Selected 2alpha-Substituted Analogues
Authors: Hourai, S. / Fujishima, T. / Kittaka, A. / Suhara, Y. / Takayama, H. / Rochel, N. / Moras, D.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)30,2962
Polymers29,8051
Non-polymers4911
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.118, 51.318, 131.284
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 / Vitamin D nuclear receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor


Mass: 29805.342 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P11473
#2: Chemical ChemComp-OCC / 2ALPHA-(3-HYDROXYPROPOXY)-1ALPHA,25-DIHYDROXYVITAMIN D3 / 9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL,2-(3-HYDROXYPROPOXY)-,(1A,2A,3B,5Z,7E)


Mass: 490.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 53.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulphate 1.4M, Mes 0.1M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 24739 / Num. obs: 24739 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 49.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 7.9 / % possible all: 100

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Processing

Software
NameClassification
ADSCdata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IE8

1ie8


Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 1171 random
Rwork0.192 --
all0.207 24435 -
obs0.192 24435 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 35 157 2196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0044
X-RAY DIFFRACTIONc_angle_deg1.017

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