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- PDB-3az1: Crystal Structure Analysis of Vitamin D receptor -

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Basic information

Entry
Database: PDB / ID: 3az1
TitleCrystal Structure Analysis of Vitamin D receptor
ComponentsVitamin D3 receptor
KeywordsHORMONE RECEPTOR / Vitamin D receptor
Function / homology
Function and homology information


regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / calcitriol binding / positive regulation of apoptotic process involved in mammary gland involution / vitamin D response element binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / calcitriol binding / positive regulation of apoptotic process involved in mammary gland involution / vitamin D response element binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / 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 / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / calcium ion transport / nuclear receptor activity / 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 / chromatin / positive regulation of gene expression / 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. / c4 zinc finger in nuclear hormone receptors ...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-DS2 / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsItoh, S. / Iijima, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Novel nonsecosteroidal vitamin D(3) carboxylic acid analogs for osteoporosis, and SAR analysis.
Authors: Kashiwagi, H. / Ono, Y. / Shimizu, K. / Haneishi, T. / Ito, S. / Iijima, S. / Kobayashi, T. / Ichikawa, F. / Harada, S. / Sato, H. / Sekiguchi, N. / Ishigai, M. / Takahashi, T.
History
DepositionMay 20, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)29,1892
Polymers28,7461
Non-polymers4431
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.613, 51.732, 131.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 28746.260 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 120-164, 216-423
Source method: isolated from a genetically manipulated source
Details: fusion protein of residues 120-164 and residues 216-423
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I1, VDR / Production host: Escherichia coli (E. coli) / References: UniProt: P11473
#2: Chemical ChemComp-DS2 / {4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}acetic acid


Mass: 442.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION PROTEIN OF RESIDUES 120-164 AND RESIDUES 216-423

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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: 2.64 Å3/Da / Density % sol: 53.43 % / Mosaicity: 0.3 °
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6 / Details: pH 6.0, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 8, 2003
RadiationMonochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 36092 / % possible obs: 99.3 %

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
BUSTER-TNTBUSTER 2.9.3refinement
PDB_EXTRACT3.1data extraction
BUSTER2.9.3refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→16.48 Å / Cor.coef. Fo:Fc: 0.9488 / Cor.coef. Fo:Fc free: 0.9446 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 1817 5.03 %RANDOM
Rwork0.1945 ---
obs0.1954 36092 72.71 %-
Displacement parametersBiso max: 97.47 Å2 / Biso mean: 31.9755 Å2 / Biso min: 14.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.8399 Å20 Å20 Å2
2---0.515 Å20 Å2
3----0.3249 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 1.5→16.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 32 235 2260
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d729SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it2064HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion268SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2654SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2064HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2795HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion15.47
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2496 12 4.76 %
Rwork0.2753 240 -
all0.2741 252 -
obs--72.71 %

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