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- PDB-3x31: Crystal structure of the human vitamin D receptor ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 3x31
TitleCrystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-14-epi-1a,25-Dihydroxy-19-norvitamin D3
ComponentsVitamin D3 receptor
KeywordsTRANSCRIPTION / hormone receptor
Function / homology
Function and homology information


: / positive regulation of vitamin D 24-hydroxylase activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity ...: / positive regulation of vitamin D 24-hydroxylase activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / phosphate ion transmembrane transport / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor 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 / retinoic acid receptor signaling pathway / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / intracellular calcium ion homeostasis / nuclear receptor activity / calcium ion transport / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / 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 / 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-41V / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKakuda, S. / Takimoto-Kamimura, M.
CitationJournal: To be Published
Title: Revisiting the 7,8-cis-vitamin D3 derivatives: synthesis, evaluating the biological activity, and study of the binding configuration
Authors: Sawada, D. / Saito, H. / Kakuda, S. / Takimoto-Kamimura, M. / Matsumoto, Y. / Takagi, K. / Ochiai, E. / Kittaka, A.
History
DepositionJan 13, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)30,2102
Polymers29,8051
Non-polymers4051
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.369, 51.508, 131.520
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: 29805.342 Da / Num. of mol.: 1
Fragment: ligand binding domain (UNP residues 118-164, 216-427)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I1, VDR / Production host: Escherichia coli (E. coli) / References: UniProt: P11473
#2: Chemical ChemComp-41V / (1R,3R,7Z,14beta,17alpha)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol


Mass: 404.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H44O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293K, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18135 / Num. obs: 18033 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→26.69 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.864 / SU B: 6.519 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.29857 917 5.1 %RANDOM
Rwork0.23666 ---
obs0.23974 17060 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.561 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2---1.98 Å2-0 Å2
3---3.83 Å2
Refinement stepCycle: LAST / Resolution: 2.11→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 29 51 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.12.0032835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4945252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85824.28691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99815383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6591513
X-RAY DIFFRACTIONr_chiral_restr0.1250.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211535
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.106→2.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 72 -
Rwork0.282 1170 -
obs--95.32 %

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