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- PDB-2zl9: 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-1... -

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Basic information

Entry
Database: PDB / ID: 2zl9
Title2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure
Components
  • Coactivator peptide DRIP
  • Vitamin D3 receptor
KeywordsHORMONE / Protein-ligand complex / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Transcription / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D binding / lithocholic acid binding / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / response to aldosterone / mammary gland branching involved in pregnancy / regulation of calcium ion transport / decidualization / negative regulation of keratinocyte proliferation / heterochromatin / nuclear retinoid X receptor binding / T-tubule / lactation / skeletal system development / apoptotic signaling pathway / animal organ morphogenesis / mRNA transcription by RNA polymerase II / cell morphogenesis / euchromatin / caveola / nuclear matrix / response to calcium ion / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to amyloid-beta / calcium ion transport / response to estradiol / heart development / sequence-specific DNA binding / cell differentiation / receptor complex / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
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-VDA / Vitamin D3 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShimizu, M. / Miyamoto, Y. / Nakabayashi, M. / Masuno, H. / Ikura, T. / Ito, N.
CitationJournal: Bioorg.Med.Chem. / Year: 2008
Title: 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation, and crystal structure
Authors: Shimizu, M. / Miyamoto, Y. / Takaku, H. / Matsuo, M. / Nakabayashi, M. / Masuno, H. / Udagawa, N. / DeLuca, H.F. / Ikura, T. / Ito, N.
History
DepositionApr 4, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: Coactivator peptide DRIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6613
Polymers32,1662
Non-polymers4951
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-9.1 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.902, 42.320, 42.130
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin D3 receptor / Ligand binding domain of vitamin D receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor / Nuclear ...Ligand binding domain of vitamin D receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor / Nuclear receptor subfamily 1 group I member 1


Mass: 30595.037 Da / Num. of mol.: 1 / Fragment: VDR-LBD, UNP residues 116-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13053
#2: Protein/peptide Coactivator peptide DRIP


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis
#3: Chemical ChemComp-VDA / (1R,2R,3R,5Z)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol / (20S)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3


Mass: 494.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H46O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.1-0.4M formic acid, 15-20% polyethylene glycol(PEG)4000, 0-20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2006
RadiationMonochromator: Triangular Si(111) with an asymmetric angle of 7.8
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 65700 / Num. obs: 24936 / % possible obs: 98.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 30.9
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2502 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RJK

1rjk


Resolution: 1.9→35.33 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 150770.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1968 9.9 %RANDOM
Rwork0.216 ---
obs0.216 19842 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6462 Å2 / ksol: 0.340841 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1--15.45 Å20 Å2-8.94 Å2
2--15.11 Å20 Å2
3---0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 34 190 2216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d10.67
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 273 9.7 %
Rwork0.358 2548 -
obs--79.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3VDX2.paramVDX2.top

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