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- PDB-9vog: Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-... -

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Basic information

Entry
Database: PDB / ID: 9vog
TitleVitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid 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 / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway / G0 to G1 transition / thyroid hormone receptor signaling pathway / response to bile acid / mammary gland branching involved in thelarche / dense fibrillar component / core mediator complex / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / vitamin D binding / calcitriol binding / cellular response to vitamin D / lithocholic acid binding / nuclear retinoic acid receptor binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of hepatocyte proliferation / ventricular trabecula myocardium morphogenesis / mediator complex / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / response to aldosterone / peroxisome proliferator activated receptor binding / phosphate ion transmembrane transport / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / negative regulation of ossification / nuclear thyroid hormone receptor binding / lens development in camera-type eye / intestinal absorption / 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 / negative regulation of neuron differentiation / epithelial cell proliferation involved in mammary gland duct elongation / histone acetyltransferase binding / erythrocyte development / LBD domain binding / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / decidualization / nuclear steroid receptor activity / regulation of calcium ion transport / monocyte differentiation / general transcription initiation factor binding / animal organ regeneration / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / nuclear retinoid X receptor binding / heterochromatin / RNA polymerase II preinitiation complex assembly / retinoic acid receptor signaling pathway / keratinocyte differentiation / intracellular receptor signaling pathway / lactation / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / T-tubule / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / cellular response to epidermal growth factor stimulus / animal organ morphogenesis / nuclear estrogen receptor binding / nuclear receptor binding / skeletal system development / transcription coregulator activity / apoptotic signaling pathway / promoter-specific chromatin binding / positive regulation of transcription elongation by RNA polymerase II / liver development / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / 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: 1.43 Å
AuthorsMudiyanselage, H.N.T.N. / Hanazono, Y. / Ito, N. / Kagechika, H. / Fujii, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Design, synthesis and structural development of nonsecosteroidal VDR ligands based on the C,C'-diphenyl-m-carborane scaffold.
Authors: Mudiyanselage, H.N.T.N. / Misawa, T. / Ochiai, K. / Demizu, Y. / Hanazono, Y. / Ito, N. / Fujii, S.
History
DepositionJul 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)32,7603
Polymers32,1662
Non-polymers5951
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-15 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.680, 42.360, 42.220
Angle α, β, γ (deg.)90.000, 96.157, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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-A1MAV / (S)-5-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}phenoxy]-4-hydroxypentanoic acid


Mass: 594.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28B10F6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium citrate tribasic monohydrate pH 8.3, 20% w/v PEG 3350

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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 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.43→38.63 Å / Num. obs: 50500 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 25.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5
Reflection shellResolution: 1.43→1.52 Å / Mean I/σ(I) obs: 0.64 / Num. unique obs: 8398 / CC1/2: 0.598

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→38.63 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.0564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 1980 3.95 %
Rwork0.1903 48120 -
obs0.1915 50100 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.61 Å2
Refinement stepCycle: LAST / Resolution: 1.43→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 43 228 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052187
X-RAY DIFFRACTIONf_angle_d1.19593062
X-RAY DIFFRACTIONf_chiral_restr0.088325
X-RAY DIFFRACTIONf_plane_restr0.0091379
X-RAY DIFFRACTIONf_dihedral_angle_d15.4907832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.470.51071300.52733210X-RAY DIFFRACTION93.14
1.47-1.510.40611390.4253395X-RAY DIFFRACTION98.47
1.51-1.550.33261400.35083416X-RAY DIFFRACTION99.52
1.55-1.60.35421410.30863410X-RAY DIFFRACTION99.38
1.6-1.660.30081410.27933432X-RAY DIFFRACTION99.69
1.66-1.720.27171410.24723433X-RAY DIFFRACTION99.44
1.72-1.80.27091420.23013434X-RAY DIFFRACTION99.89
1.8-1.90.29411420.24373443X-RAY DIFFRACTION99.78
1.9-2.020.241450.20213482X-RAY DIFFRACTION99.78
2.02-2.170.21331410.18763421X-RAY DIFFRACTION99.86
2.17-2.390.21581440.18683491X-RAY DIFFRACTION99.95
2.39-2.730.22771430.18933460X-RAY DIFFRACTION99.89
2.74-3.450.20651420.18083499X-RAY DIFFRACTION99.92
3.45-38.630.18251490.15233594X-RAY DIFFRACTION99.84

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