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- PDB-5nky: Structure-activity relationship study of vitamin D analogs with o... -

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Basic information

Entry
Database: PDB / ID: 5nky
TitleStructure-activity relationship study of vitamin D analogs with oxolane group in their side chain
Components
  • SRC1
  • Vitamin D3 receptor A
KeywordsGENE REGULATION
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / Nuclear Receptor transcription pathway / SUMOylation of intracellular receptors / calcitriol binding / lithocholic acid binding / hematopoietic stem cell proliferation / vitamin D binding / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity ...heart jogging / Vitamin D (calciferol) metabolism / Nuclear Receptor transcription pathway / SUMOylation of intracellular receptors / calcitriol binding / lithocholic acid binding / hematopoietic stem cell proliferation / vitamin D binding / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / heart looping / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / male mating behavior / progesterone receptor signaling pathway / response to progesterone / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cerebellum development / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / protein-lysine-acetyltransferase activity / nuclear retinoid X receptor binding / lactation / positive regulation of neuron differentiation / estrous cycle / ossification / estrogen receptor signaling pathway / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / calcium ion homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / intracellular receptor signaling pathway / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / positive regulation of adipose tissue development / bile acid and bile salt transport / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / male gonad development / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coregulator activity / response to estradiol / transcription regulator complex / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Estrogen-dependent gene expression / cell differentiation / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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-91W / Nuclear receptor coactivator 1 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsRochel, N. / Belorusova, A.Y.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0024-01 France
FRM(FRM: FDT20140930978 France
CitationJournal: Eur J Med Chem / Year: 2017
Title: Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain.
Authors: Belorusova, A.Y. / Martinez, A. / Gandara, Z. / Gomez, G. / Fall, Y. / Rochel, N.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor A
B: SRC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2813
Polymers35,8372
Non-polymers4451
Water27015
1
A: Vitamin D3 receptor A
B: SRC1
hetero molecules

A: Vitamin D3 receptor A
B: SRC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5636
Polymers71,6734
Non-polymers8892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area3980 Å2
ΔGint-30 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.191, 66.191, 261.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vitamin D3 receptor A / VDR-A / 1 / 25-dihydroxyvitamin D3 receptor A / Nuclear receptor subfamily 1 group I member 1-A


Mass: 34060.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTN2
#2: Protein/peptide SRC1


Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS
#3: Chemical ChemComp-91W / (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol


Mass: 444.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M BTP pH 7.0, 3 M NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.096→50 Å / Num. obs: 17559 / % possible obs: 84 % / Redundancy: 15.3 % / Rsym value: 0.087 / Net I/σ(I): 27
Reflection shellResolution: 2.096→2.14 Å / Redundancy: 8.8 % / Rsym value: 0.553 / % possible all: 31

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Processing

Software
NameVersionClassification
PHENIXdev_1980refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2.096→43.616 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 859 4.91 %RANDOM SELECTION
Rwork0.2262 ---
obs0.2272 17505 83.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.096→43.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 32 15 2032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072058
X-RAY DIFFRACTIONf_angle_d0.9932780
X-RAY DIFFRACTIONf_dihedral_angle_d14.738799
X-RAY DIFFRACTIONf_chiral_restr0.041318
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0961-2.22740.4189550.28581126X-RAY DIFFRACTION35
2.2274-2.39940.313930.30652164X-RAY DIFFRACTION66
2.3994-2.64080.3091620.28533170X-RAY DIFFRACTION97
2.6408-3.02280.26721620.28523295X-RAY DIFFRACTION99
3.0228-3.80810.281920.2433308X-RAY DIFFRACTION100
3.8081-43.62580.2091950.1913583X-RAY DIFFRACTION100

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