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- PDB-8iqt: Crystal structure of the human vitamin D receptor ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 8iqt
TitleCrystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3
ComponentsVitamin D3 receptor
KeywordsTRANSCRIPTION / nuclear 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 / 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 / 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 ...Vitamin D receptor / VDR, DNA-binding domain / 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
Similarity search - Domain/homology
: / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.745 Å
AuthorsKakuda, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3
Authors: Kakuda, S.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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)34,8212
Polymers34,4021
Non-polymers4191
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.723, 51.363, 132.102
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: 34401.973 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) / References: UniProt: P11473
#2: Chemical ChemComp-SV0 / (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},4~{R})-4-fluoranyl-6-methyl-6-oxidanyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol


Mass: 418.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H43FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.745→47.9 Å / Num. obs: 59041 / % possible obs: 98.8 % / Redundancy: 1.37 % / CC1/2: 0.842 / Net I/σ(I): 13.67
Reflection shellResolution: 1.75→1.85 Å / Num. unique obs: 9081 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.745→47.872 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.179 / SU B: 2.274 / SU ML: 0.071 / Average fsc free: 0.9684 / Average fsc work: 0.9756 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2071 1559 4.962 %
Rwork0.1816 29857 -
all0.183 --
obs-31416 98.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0 Å2-0 Å2
2---0.001 Å2-0 Å2
3---0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.745→47.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 30 107 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162036
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.672837
X-RAY DIFFRACTIONr_angle_other_deg0.5711.6014711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.295252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54810383
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.7121091
X-RAY DIFFRACTIONr_chiral_restr0.0860.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022371
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02445
X-RAY DIFFRACTIONr_nbd_refined0.240.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21849
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21087
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.27
X-RAY DIFFRACTIONr_nbd_other0.1950.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.28
X-RAY DIFFRACTIONr_mcbond_it2.522.4291014
X-RAY DIFFRACTIONr_mcbond_other2.4172.4251013
X-RAY DIFFRACTIONr_mcangle_it3.424.3491264
X-RAY DIFFRACTIONr_mcangle_other3.4244.351265
X-RAY DIFFRACTIONr_scbond_it4.0992.9011080
X-RAY DIFFRACTIONr_scbond_other4.0972.91081
X-RAY DIFFRACTIONr_scangle_it6.2545.0981573
X-RAY DIFFRACTIONr_scangle_other6.2525.0961574
X-RAY DIFFRACTIONr_lrange_it7.13924.5812400
X-RAY DIFFRACTIONr_lrange_other7.12924.4532386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.745-1.790.302880.29419490.29423280.9440.94287.50.265
1.79-1.8390.2761170.26320670.26322440.9510.95597.32620.221
1.839-1.8930.239950.22220510.22321610.960.96799.30590.182
1.893-1.9510.2381040.18920380.19221420.9590.9761000.156
1.951-2.0150.2281060.17819420.18120480.9680.9791000.155
2.015-2.0850.2281190.17718930.1820120.9710.9811000.156
2.085-2.1640.221090.17318240.17519330.9710.9821000.154
2.164-2.2520.196800.17917980.1818780.9760.9811000.158
2.252-2.3520.169950.16217080.16218030.980.9841000.147
2.352-2.4660.228980.17716070.1817050.9670.981000.164
2.466-2.60.194680.17715670.17816350.9760.9811000.165
2.6-2.7570.216760.17514760.17715520.9720.9811000.163
2.757-2.9460.202790.17913960.1814750.9730.9811000.173
2.946-3.1810.184610.1813080.1813690.980.9791000.178
3.181-3.4830.164590.17312100.17312700.9820.98299.92130.177
3.483-3.8920.181600.1711010.1711610.9810.9841000.178
3.892-4.4890.19460.1549940.15510400.980.9871000.17
4.489-5.4860.216390.1848370.1858760.9810.9841000.212
5.486-7.7080.288360.2356770.2377130.9550.9751000.255
7.708-47.8720.211240.1744140.1764380.9710.9761000.223

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