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- PDB-1txi: Crystal structure of the vdr ligand binding domain complexed to TX522 -

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Basic information

Entry
Database: PDB / ID: 1txi
TitleCrystal structure of the vdr ligand binding domain complexed to TX522
ComponentsVitamin D receptor
KeywordsGENE REGULATION / VDR ligand binding domain / TX522 complex / nuclear receptor / transcription regulation / alpha-helical sandwich
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 / lithocholic acid 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 / lithocholic acid binding / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / positive regulation of 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 / Nuclear Receptor transcription pathway / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / calcium ion transport / 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. ...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-TX5 / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoras, D. / Rochel, N.
CitationJournal: Mol.Pharmacol. / Year: 2005
Title: Superagonistic Action of 14-epi-Analogs of 1,25-Dihydroxyvitamin D Explained by Vitamin D Receptor-Coactivator Interaction
Authors: Eelen, G. / Verlinden, L. / Rochel, N. / Claessens, F. / De Clercq, P. / Vandewalle, M. / Tocchini-Valentini, G. / Moras, D. / Bouillon, R. / Verstuyf, A.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 2.0Nov 4, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.pdbx_synonyms / _entity.formula_weight / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
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 D receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2062
Polymers29,8051
Non-polymers4011
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.259, 52.504, 132.930
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 D receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor


Mass: 29805.342 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P11473
#2: Chemical ChemComp-TX5 / (1R,3R)-5-((Z)-2-((1R,7AS)-HEXAHYDRO-1-((S)-6-HYDROXY-6-METHYLHEPT-4-YN-2-YL)-7A-METHYL-1H-INDEN-4(7AH)-YLIDENE)ETHYLIDENE)CYCLOHEXANE-1,3-DIOL / 19-NOR-14-EPI-23-YNE-1,25 DIHYDROXYVITAMIN D3 / TX522


Mass: 400.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H40O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.918 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 30, 1999 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.84→25 Å / Num. all: 26792 / Num. obs: 26792 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.05
Reflection shellResolution: 1.84→1.88 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.262 / % possible all: 98

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2425 -random
Rwork0.191 ---
obs0.191 24507 95.3 %-
all-24507 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.56 Å2--
2--0.44 Å2-
3----1.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 29 135 2176
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.232 341 -
Rwork0.206 --
obs-3200 84.1 %

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