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- PDB-7c7w: Vitamin D3 receptor/lithochoric acid derivative complex -

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Basic information

Entry
Database: PDB / ID: 7c7w
TitleVitamin D3 receptor/lithochoric acid derivative complex
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 / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors ...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 / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors / G0 to G1 transition / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid / 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 / 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 / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of ossification / vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / positive regulation of vitamin D receptor signaling pathway / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / response to aldosterone / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / 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 keratinocyte proliferation / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / T-tubule / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / lactation / Regulation of lipid metabolism by PPARalpha / positive regulation of erythrocyte differentiation / liver development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / apoptotic signaling pathway / skeletal system development / nuclear receptor binding / nuclear estrogen receptor binding / promoter-specific chromatin binding / animal organ morphogenesis / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / brain development / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / euchromatin / caveola / 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 / Zinc finger, C4 type (two domains) ...: / 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 / 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
Similarity search - Domain/homology
Chem-FKF / FORMIC ACID / 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: 1.9 Å
AuthorsMasuno, H. / Numoto, N. / Kagechika, H. / Ito, N.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists.
Authors: Sasaki, H. / Masuno, H. / Kawasaki, H. / Yoshihara, A. / Numoto, N. / Ito, N. / Ishida, H. / Yamamoto, K. / Hirata, N. / Kanda, Y. / Kawachi, E. / Kagechika, H. / Tanatani, A.
History
DepositionMay 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
C: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6454
Polymers32,1662
Non-polymers4792
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-10 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.144, 37.436, 40.910
Angle α, β, γ (deg.)90.000, 98.581, 90.000
Int Tables number5
Space group name H-MC121

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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 / Mutation: deletion 166-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / 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-FKF / (4R)-4-[(3S,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid


Mass: 432.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 18622 / % possible obs: 98.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rsym value: 0.069 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.7 % / Num. unique obs: 2898 / CC1/2: 0.783 / Rsym value: 0.763 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.387 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.248 937 5.033 %
Rwork0.1912 17680 -
all0.194 --
obs-18617 98.644 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 39.447 Å2
Baniso -1Baniso -2Baniso -3
1--3.413 Å20 Å2-1.368 Å2
2--1.451 Å20 Å2
3---2.271 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 34 16 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132001
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171915
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6642709
X-RAY DIFFRACTIONr_angle_other_deg1.3321.6124476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5165237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71523.54296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76415369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.628159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_nbd_refined0.2120.2447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.21862
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2992
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.246
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.214
X-RAY DIFFRACTIONr_nbd_other0.1630.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.23
X-RAY DIFFRACTIONr_mcbond_it3.0413.941960
X-RAY DIFFRACTIONr_mcbond_other3.043.943961
X-RAY DIFFRACTIONr_mcangle_it4.3745.8821193
X-RAY DIFFRACTIONr_mcangle_other4.3725.8841194
X-RAY DIFFRACTIONr_scbond_it4.1594.4671041
X-RAY DIFFRACTIONr_scbond_other4.1564.4641040
X-RAY DIFFRACTIONr_scangle_it6.3026.4851516
X-RAY DIFFRACTIONr_scangle_other6.36.4861517
X-RAY DIFFRACTIONr_lrange_it7.98447.2372206
X-RAY DIFFRACTIONr_lrange_other7.98447.2352206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.355730.3951209X-RAY DIFFRACTION91.5714
1.95-2.0030.369630.331258X-RAY DIFFRACTION99.398
2.003-2.0610.266690.2781252X-RAY DIFFRACTION99.6229
2.061-2.1240.265630.2491207X-RAY DIFFRACTION99.4518
2.124-2.1940.223520.2271168X-RAY DIFFRACTION99.5106
2.194-2.2710.238620.2091115X-RAY DIFFRACTION99.3249
2.271-2.3570.27640.1971081X-RAY DIFFRACTION99.6519
2.357-2.4530.262630.1931044X-RAY DIFFRACTION99.1936
2.453-2.5620.186510.1721009X-RAY DIFFRACTION99.344
2.562-2.6870.268450.159966X-RAY DIFFRACTION98.9237
2.687-2.8320.247470.157921X-RAY DIFFRACTION99.5885
2.832-3.0030.303440.183863X-RAY DIFFRACTION99.2341
3.003-3.210.257430.187823X-RAY DIFFRACTION99.1982
3.21-3.4670.252450.172762X-RAY DIFFRACTION99.3842
3.467-3.7970.186360.167711X-RAY DIFFRACTION99.4674
3.797-4.2440.221320.162651X-RAY DIFFRACTION98.6994
4.244-4.8980.151270.156549X-RAY DIFFRACTION98.6301
4.898-5.9930.346260.223497X-RAY DIFFRACTION98.1238
5.993-8.450.304210.195370X-RAY DIFFRACTION97.75
8.45-400.257110.195224X-RAY DIFFRACTION95.9184

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