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- PDB-7c7v: Vitamin D3 receptor/lithochoric acid derivative complex -

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Basic information

Entry
Database: PDB / ID: 7c7v
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 / retinal pigment epithelium development / SUMOylation of intracellular receptors / mammary gland branching involved in thelarche ...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 / retinal pigment epithelium development / SUMOylation of intracellular receptors / mammary gland branching involved in thelarche / 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 / 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 / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of hepatocyte proliferation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / nuclear thyroid hormone receptor binding / intestinal absorption / negative regulation of ossification / lens development in camera-type eye / embryonic hemopoiesis / positive regulation of intracellular estrogen receptor signaling pathway / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / histone acetyltransferase binding / response to aldosterone / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / 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 / negative regulation of keratinocyte proliferation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / ubiquitin ligase complex / erythrocyte development / animal organ regeneration / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / heterochromatin / retinoic acid receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / : / T-tubule / lactation / Regulation of lipid metabolism by PPARalpha / 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 / promoter-specific chromatin binding / transcription coregulator activity / apoptotic signaling pathway / transcription coactivator binding / mRNA transcription by RNA polymerase II / Heme signaling / protein-DNA complex / Transcriptional activation of mitochondrial biogenesis / euchromatin
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
Chem-FKC / 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: 2 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
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.045, 36.898, 39.486
Angle α, β, γ (deg.)90.000, 96.963, 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-FKC / (4R)-4-[(3R,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: isolated from a genetically manipulated source
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.: 9 / 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: 1.78 Å3/Da / Density % sol: 30.76 %
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 PILATUS 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: 2→40 Å / Num. obs: 15052 / % possible obs: 97.4 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rsym value: 0.094 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2325 / CC1/2: 0.91 / Rsym value: 0.63

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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: 2→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.883 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.23 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2678 762 5.068 %
Rwork0.1977 14274 -
all0.201 --
obs-15036 97.339 %
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: 44.663 Å2
Baniso -1Baniso -2Baniso -3
1--5.813 Å20 Å2-0.931 Å2
2--3.688 Å20 Å2
3---2.284 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 34 9 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171935
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6622759
X-RAY DIFFRACTIONr_angle_other_deg1.3331.614521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5323.60897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.415159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2120.2480
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21799
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21027
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.216
X-RAY DIFFRACTIONr_nbd_other0.2460.267
X-RAY DIFFRACTIONr_mcbond_it3.5434.582985
X-RAY DIFFRACTIONr_mcbond_other3.5424.583986
X-RAY DIFFRACTIONr_mcangle_it5.0546.8481226
X-RAY DIFFRACTIONr_mcangle_other5.0526.8491227
X-RAY DIFFRACTIONr_scbond_it4.4394.9981049
X-RAY DIFFRACTIONr_scbond_other4.4364.9941048
X-RAY DIFFRACTIONr_scangle_it6.5777.3051533
X-RAY DIFFRACTIONr_scangle_other6.5757.3061534
X-RAY DIFFRACTIONr_lrange_it8.28655.5732280
X-RAY DIFFRACTIONr_lrange_other8.28455.5682281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.006-2.0580.389590.376981X-RAY DIFFRACTION91.3082
2.058-2.1140.382470.3641001X-RAY DIFFRACTION97.3073
2.114-2.1750.346510.3381025X-RAY DIFFRACTION98.1752
2.175-2.2420.264510.317939X-RAY DIFFRACTION97.3451
2.242-2.3160.298550.259949X-RAY DIFFRACTION97.9512
2.316-2.3970.266540.223878X-RAY DIFFRACTION97.1846
2.397-2.4870.259480.208901X-RAY DIFFRACTION98.1386
2.487-2.5890.31440.198843X-RAY DIFFRACTION98.4462
2.589-2.7040.325420.2827X-RAY DIFFRACTION98.4145
2.704-2.8350.249380.176796X-RAY DIFFRACTION98.9324
2.835-2.9890.264380.172722X-RAY DIFFRACTION98.0645
2.989-3.170.24320.178709X-RAY DIFFRACTION98.4064
3.17-3.3880.275450.186667X-RAY DIFFRACTION97.8022
3.388-3.6590.187320.162618X-RAY DIFFRACTION97.8916
3.659-4.0070.196230.158551X-RAY DIFFRACTION94.5634
4.007-4.4790.221340.153508X-RAY DIFFRACTION96.6132
4.479-5.1690.196220.145462X-RAY DIFFRACTION98.374
5.169-6.3240.424210.221395X-RAY DIFFRACTION98.3452
6.324-8.9140.333160.201314X-RAY DIFFRACTION97.9229
8.914-400.254100.188188X-RAY DIFFRACTION99

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