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- PDB-9m1d: Vitamin D receptor complex with a methyldiphenylpropylsilane deri... -

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Basic information

Entry
Database: PDB / ID: 9m1d
TitleVitamin D receptor complex with a methyldiphenylpropylsilane derivative
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / Vitamin D receptor
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / core mediator complex / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / cellular response to vitamin D / vitamin D binding / calcitriol binding / lithocholic acid binding / nuclear retinoic acid receptor binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / phosphate ion transmembrane transport / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / positive regulation of hepatocyte proliferation / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / intestinal absorption / nuclear thyroid hormone receptor binding / negative regulation of ossification / lens development in camera-type eye / embryonic hemopoiesis / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / response to aldosterone / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / regulation of calcium ion transport / decidualization / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of keratinocyte proliferation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / animal organ regeneration / erythrocyte development / nuclear retinoid X receptor binding / heterochromatin / retinoic acid receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / intracellular receptor signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / T-tubule / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / animal organ morphogenesis / nuclear receptor binding / skeletal system development / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / apoptotic signaling pathway / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / euchromatin / PPARA activates gene expression
Similarity search - Function
: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type ...: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / 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
Similarity search - Domain/homology
: / Vitamin D3 receptor / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsThilakarathne, N.M.H.N. / Hanazono, Y. / Ito, N. / Kagechika, H. / Fujii, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Bioorg.Med.Chem. / Year: 2025
Title: Structure-activity relationship and crystallographic analyses of non-secosteroidal vitamin D receptor ligands bearing diphenylsilane core as a hydrophobic pharmacophore
Authors: Mudiyanselage, H.N.T.N. / Misawa, T. / Ochiai, K. / Demizu, Y. / Hanazono, Y. / Ito, N. / Fujii, S.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6833
Polymers32,1662
Non-polymers5171
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.850, 42.210, 42.250
Angle α, β, γ (deg.)90.000, 95.831, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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: 30595.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-A1L8B / (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-methyl-propyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid


Mass: 516.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H44O6Si / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 3350, Lithium citrate tribasic tetrahydrate, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.44→38.59 Å / Num. obs: 49004 / % possible obs: 99.1 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.18
Reflection shellResolution: 1.44→1.53 Å / Mean I/σ(I) obs: 0.63 / Num. unique obs: 8052 / CC1/2: 0.611 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 1.44→38.58 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9623 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2104 1995 4.09 %
Rwork0.1786 46814 -
obs0.1799 48809 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.47 Å2
Refinement stepCycle: LAST / Resolution: 1.44→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 36 217 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872286
X-RAY DIFFRACTIONf_angle_d1.0273123
X-RAY DIFFRACTIONf_chiral_restr0.0759347
X-RAY DIFFRACTIONf_plane_restr0.0065407
X-RAY DIFFRACTIONf_dihedral_angle_d25.0734888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.48861380.46263251X-RAY DIFFRACTION95.95
1.48-1.520.45561400.40733300X-RAY DIFFRACTION97.81
1.52-1.560.36891400.3553287X-RAY DIFFRACTION98.11
1.56-1.610.29771420.29293316X-RAY DIFFRACTION98.38
1.61-1.670.29061400.26723295X-RAY DIFFRACTION98.4
1.67-1.740.26891420.22663296X-RAY DIFFRACTION98.54
1.74-1.810.21541430.20393375X-RAY DIFFRACTION98.88
1.81-1.910.24031420.18763325X-RAY DIFFRACTION98.89
1.91-2.030.21081420.1723339X-RAY DIFFRACTION99.09
2.03-2.190.18861430.16313358X-RAY DIFFRACTION99.21
2.19-2.410.19351440.16943361X-RAY DIFFRACTION99.52
2.41-2.750.2071440.17063384X-RAY DIFFRACTION99.63
2.75-3.470.18231460.16323438X-RAY DIFFRACTION99.78
3.47-38.580.1891490.1463489X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.164490139580.5529616029180.2718883191241.24097515498-0.02405860165071.44014979750.0559742738203-0.140836965036-0.09707175336780.0640423450204-0.0482565573831-0.0493035831073-0.09131585668850.06682172078820.003926815814840.190920161557-0.0316789134636-0.0153212011640.218515332328-0.0005567348719880.17424991587719.0255760660.37054229911119.7383705119
27.66365771309-0.7710172894141.511802998694.66709051010.8940161314894.57710769852-0.03603004070270.129319897579-0.755816397218-0.1354370581010.01044143621370.1241353018170.505210496722-0.302489330135-0.002005956624620.28432431631-0.005918165528760.03115099828360.417497426039-0.06977301833170.3651494326475.57766391047-10.841377990210.9388237506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain C

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