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- PDB-7vqp: Vitamin D receptor complexed with a lithocholic acid derivative -

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Basic information

Entry
Database: PDB / ID: 7vqp
TitleVitamin D receptor complexed with a lithocholic acid derivative
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / vitamin D Receptor / lithocholic acid
Function / homology
Function and homology information


enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / lens development in camera-type eye / nuclear thyroid hormone receptor binding / embryonic hemopoiesis / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / general transcription initiation factor binding / negative regulation of neuron differentiation / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / animal organ regeneration / ubiquitin ligase complex / intracellular steroid hormone receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / nuclear estrogen receptor binding / promoter-specific chromatin binding / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / brain development / Heme signaling / mRNA transcription by RNA polymerase II / cell morphogenesis / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / Circadian Clock / angiogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus
Similarity search - Function
Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Domain/homology
Chem-7SW / 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: 1.94 Å
AuthorsKato, K. / Numoto, N. / Kagechika, H. / Tanatani, A. / Ito, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2022
Title: Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists.
Authors: Yoshihara, A. / Kawasaki, H. / Masuno, H. / Takada, K. / Numoto, N. / Ito, N. / Hirata, N. / Kanda, Y. / Ishizawa, M. / Makishima, M. / Kagechika, H. / Tanatani, A.
History
DepositionOct 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)32,6703
Polymers32,1662
Non-polymers5041
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.805, 37.581, 40.913
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin D3 receptor


Mass: 30595.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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-7SW / 3-((R)-4-((3R,5R,8R,9S,10S,13R,14S,17R)-3-(2-hydroxy-2-methylpropyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanamido)propanoic acid


Mass: 503.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H53NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.86 Å3/Da / Density % sol: 34.04 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MOPS-NaOH, 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, 5% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.94→40 Å / Num. obs: 17530 / % possible obs: 98.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rsym value: 0.056 / Net I/σ(I): 8.6
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1183 / CC1/2: 0.876 / Rsym value: 0.567 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 1.94→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.607 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 848 4.839 %
Rwork0.207 16675 -
all0.209 --
obs-17523 98.058 %
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: 33.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.109 Å20 Å2-0.06 Å2
2---0.11 Å2-0 Å2
3---0.018 Å2
Refinement stepCycle: LAST / Resolution: 1.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 36 10 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161972
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.6672727
X-RAY DIFFRACTIONr_angle_other_deg1.3061.6194574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26823.54296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.235159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined0.2080.2458
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.21823
X-RAY DIFFRACTIONr_nbtor_refined0.160.2979
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.29
X-RAY DIFFRACTIONr_nbd_other0.1620.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.22
X-RAY DIFFRACTIONr_mcbond_it2.5643.323965
X-RAY DIFFRACTIONr_mcbond_other2.5623.32964
X-RAY DIFFRACTIONr_mcangle_it3.6924.9531201
X-RAY DIFFRACTIONr_mcangle_other3.6914.9561202
X-RAY DIFFRACTIONr_scbond_it3.4053.771048
X-RAY DIFFRACTIONr_scbond_other3.4013.7681047
X-RAY DIFFRACTIONr_scangle_it5.1765.4761526
X-RAY DIFFRACTIONr_scangle_other5.1745.4771527
X-RAY DIFFRACTIONr_lrange_it6.6939.8262198
X-RAY DIFFRACTIONr_lrange_other6.68839.8412199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.454590.3371228X-RAY DIFFRACTION98.0198
1.99-2.0450.347590.3221193X-RAY DIFFRACTION98.6604
2.045-2.1040.318610.2821092X-RAY DIFFRACTION94.9753
2.104-2.1680.282570.2381136X-RAY DIFFRACTION99.0042
2.168-2.2390.31520.2211112X-RAY DIFFRACTION98.5605
2.239-2.3180.245610.2041052X-RAY DIFFRACTION97.7173
2.318-2.4050.249540.1981014X-RAY DIFFRACTION98.524
2.405-2.5030.298450.193978X-RAY DIFFRACTION97.2433
2.503-2.6130.251340.19952X-RAY DIFFRACTION98.5015
2.613-2.740.246480.184907X-RAY DIFFRACTION97.9487
2.74-2.8880.31420.189887X-RAY DIFFRACTION99.8925
2.888-3.0620.255390.199820X-RAY DIFFRACTION99.652
3.062-3.2720.231490.199763X-RAY DIFFRACTION99.388
3.272-3.5320.279390.213710X-RAY DIFFRACTION97.2727
3.532-3.8660.238370.201667X-RAY DIFFRACTION98.4615
3.866-4.3180.186280.181598X-RAY DIFFRACTION97.9656
4.318-4.9760.158350.171519X-RAY DIFFRACTION94.863
4.976-6.0710.194200.243464X-RAY DIFFRACTION98.374
6.071-8.4880.243220.197356X-RAY DIFFRACTION98.1818
8.488-400.17670.183227X-RAY DIFFRACTION97.0954

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