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- PDB-1db1: CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1db1
TitleCRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D
ComponentsVITAMIN D NUCLEAR RECEPTOR
KeywordsGENE REGULATION / 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 / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / 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 / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / 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 / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / 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 / chromatin / positive regulation of gene expression / 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-VDX / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRochel, N. / Wurtz, J.M. / Mitschler, A. / Klaholz, B. / Moras, D.
CitationJournal: Mol.Cell / Year: 2000
Title: The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand.
Authors: Rochel, N. / Wurtz, J.M. / Mitschler, A. / Klaholz, B. / Moras, D.
History
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 D NUCLEAR RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8092
Polymers29,3921
Non-polymers4171
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.193, 52.443, 133.286
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 NUCLEAR RECEPTOR / VDR


Mass: 29391.871 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P11473
#2: Chemical ChemComp-VDX / 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL / 1,25 DIHYDROXY VITAMIN D3 / Calcitriol


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, mes, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14-10 mg/mlprotein1drop
20.7 Mammonium sulfate1drop
350 mMMES1drop
45 mMTris-HCl1drop
55 mMdithiothreitol1drop
61.4 Mammonium sulfate1reservoir
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 30148 / Num. obs: 29434 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.24 / % possible all: 95.3
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2879 -random
Rwork0.191 ---
all-30148 --
obs-28808 95.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 30 164 2186
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.083
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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