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- PDB-5yt2: Crystal structure of the human vitamin D receptor ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 5yt2
TitleCrystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol
ComponentsVitamin D3 receptor
KeywordsTRANSCRIPTION / Active ligand / Complex
Function / homology
Function and homology information


response to bile acid / Vitamin D (calciferol) metabolism / calcitriol binding / lithocholic acid binding / vitamin D metabolic process / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / negative regulation of keratinocyte proliferation / vitamin D binding ...response to bile acid / Vitamin D (calciferol) metabolism / calcitriol binding / lithocholic acid binding / vitamin D metabolic process / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / negative regulation of keratinocyte proliferation / vitamin D binding / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / phosphate ion transmembrane transport / positive regulation of bone mineralization / decidualization / nuclear steroid receptor activity / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / cell morphogenesis / intracellular receptor signaling pathway / SUMOylation of intracellular receptors / RNA polymerase II transcription regulator complex / Nuclear Receptor transcription pathway / mRNA transcription by RNA polymerase II / nuclear receptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / signaling receptor complex / 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 / nucleoplasm / zinc ion binding / nucleus / cytoplasm
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 / Double treble clef zinc finger, C4 type / 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 / Double treble clef zinc finger, C4 type / 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-90O / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTakimoto-Kamimura, M. / Kakuda, S.
CitationJournal: Org. Biomol. Chem. / Year: 2018
Title: Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.
Authors: Sawada, D. / Kakuda, S. / Takeuchi, A. / Kawagoe, F. / Takimoto-Kamimura, M. / Kittaka, A.
History
DepositionNov 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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)29,4092
Polymers28,9481
Non-polymers4611
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.565, 51.565, 132.490
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: 28948.420 Da / Num. of mol.: 1 / Fragment: ligand binding domain
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-90O / (1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol / (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol


Mass: 460.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H48O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 53.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50mM Mes, 1.4M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21508 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 40.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.366

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALA3.3.20data scaling
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DB1

1db1


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.587 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.161
Details: 1. 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: 1. 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. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23342 1100 5.1 %RANDOM
Rwork0.19119 ---
obs0.19338 20336 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 33 151 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9963043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93324.216102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42815411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921516
X-RAY DIFFRACTIONr_chiral_restr0.1440.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021694
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21068
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21574
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2141.51414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92722218
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5993924
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8514.5825
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 77 -
Rwork0.19 1461 -
obs--98.72 %

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