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- PDB-5gt4: Crystal structure of the human vitamin D receptor ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 5gt4
TitleCrystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol
ComponentsVitamin D3 receptor
KeywordsTRANSCRIPTION / nuclear hormone receptor full agonist ligand complex
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 / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / 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 / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / 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 / intestinal absorption / bile acid signaling pathway / 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 / 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. / 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-2KB / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsTakimoto-Kamimura, M.
CitationJournal: To Be Published
Title: Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol
Authors: Takimoto-Kamimura, M.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 9, 2016ID: 4PA2
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,4482
Polymers28,9481
Non-polymers5001
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.663, 51.842, 131.475
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: 28948.420 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 118-164,216-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDR, NR1I1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11473
#2: Chemical ChemComp-2KB / 4-{[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}butanenitrile


Mass: 499.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H49NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 53.21 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5 / Details: 50mM Mes, 1.4M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.827→65.738 Å / Num. all: 27881 / Num. obs: 27881 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.103 / Rsym value: 0.095 / Net I/av σ(I): 6.342 / Net I/σ(I): 13.9 / Num. measured all: 199736
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.83-1.9370.471.6198.6
1.93-2.047.30.2982.51100
2.04-2.187.30.1993.81100
2.18-2.367.30.1395.31100
2.36-2.587.30.1116.71100
2.58-2.897.20.08781100
2.89-3.347.20.0758.81100
3.34-4.097.10.0699.51100
4.09-5.786.80.05112.21100
5.78-48.2286.50.04610.7199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation42.29 Å2.1 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DB1

1db1


Resolution: 1.83→48.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.414 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.116
Details: The authors state they removed the long loop 165-215 for the crystallization with direct lincage with Gly 164 and Ser 216, so this region recieved quite large steric hindrance and resuled ...Details: The authors state they removed the long loop 165-215 for the crystallization with direct lincage with Gly 164 and Ser 216, so this region recieved quite large steric hindrance and resuled abnormal bond length as usual, and that the bond is existing in real but the bond distance is abnormal by the disorder by the steric hindrances.
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1394 5 %RANDOM
Rwork0.1904 ---
obs0.1918 26427 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.91 Å2 / Biso mean: 19.969 Å2 / Biso min: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3---1.35 Å2
Refinement stepCycle: final / Resolution: 1.83→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 36 71 2134
Biso mean--15.52 21.09 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192145
X-RAY DIFFRACTIONr_bond_other_d0.0010.022093
X-RAY DIFFRACTIONr_angle_refined_deg2.2442.0052909
X-RAY DIFFRACTIONr_angle_other_deg1.05734842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35824.25594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67515393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9691514
X-RAY DIFFRACTIONr_chiral_restr0.1470.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212372
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02464
LS refinement shellResolution: 1.827→1.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 89 -
Rwork0.23 1883 -
all-1972 -
obs--97 %

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