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- PDB-5e7v: Potent Vitamin D Receptor Agonist -

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Basic information

Entry
Database: PDB / ID: 5e7v
TitlePotent Vitamin D Receptor Agonist
Components
  • Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / Vitamin D nuclear receptor / VDR / ligand binding domain
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hematopoietic stem cell proliferation / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / heart looping / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / calcium ion homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / ossification / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / cell differentiation / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Nuclear receptor coactivator, interlocking / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-ALPHA-HYDROXY-27-NOR-25-O-CARBONYL-VITAMIN D3 / Nuclear receptor coactivator 1 / Nuclear receptor coactivator 1 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOtero, R. / Seoane, S. / Sigueiro, R. / Belorusova, A.Y. / Maestro, M.A. / Perez-Fernandez, R. / Rochel, N. / Mourino, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0024-01 France
CitationJournal: Chem Sci / Year: 2016
Title: Carborane-based design of a potent vitamin D receptor agonist.
Authors: Otero, R. / Seoane, S. / Sigueiro, R. / Belorusova, A.Y. / Maestro, M.A. / Perez-Fernandez, R. / Rochel, N. / Mourino, A.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 A
B: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1823
Polymers35,6932
Non-polymers4901
Water1,60389
1
A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 1
hetero molecules

A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3656
Polymers71,3854
Non-polymers9792
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area3880 Å2
ΔGint-29 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.490, 66.490, 263.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vitamin D3 receptor A / VDR-A / 1 / 25-dihydroxyvitamin D3 receptor A / Nuclear receptor subfamily 1 group I member 1-A


Mass: 33916.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTN2
#2: Protein/peptide Nuclear receptor coactivator 1 /


Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B5MCN7, UniProt: Q15788*PLUS
#3: Chemical ChemComp-M7E / 1-ALPHA-HYDROXY-27-NOR-25-O-CARBONYL-VITAMIN D3


Mass: 489.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H37B10O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: li sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07207 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07207 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 14509 / % possible obs: 97.3 % / Redundancy: 8.2 % / Biso Wilson estimate: 55.36 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 24
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.285 / % possible all: 79.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2.4→24.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9254 / SU R Cruickshank DPI: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 700 5 %RANDOM
Rwork0.1856 ---
obs0.1869 13990 97.31 %-
Displacement parametersBiso mean: 62.2 Å2
Baniso -1Baniso -2Baniso -3
1--8.9234 Å20 Å20 Å2
2---8.9234 Å20 Å2
3---17.8468 Å2
Refine analyzeLuzzati coordinate error obs: 0.357 Å
Refinement stepCycle: 1 / Resolution: 2.4→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 38 89 2124
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012143HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.863053HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d795SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes299HARMONIC5
X-RAY DIFFRACTIONt_it2143HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion22.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2530SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.59 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2484 131 5.28 %
Rwork0.2005 2351 -
all0.2031 2482 -
obs--97.31 %
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)
13.5277-0.6135-1.40531.98791.31972.32810.0579-0.25430.30760.0443-0.037-0.0405-0.0152-0.2276-0.021-0.1643-0.00580.01290.0651-0.0793-0.0504-39.465230.8545-2.3994
24.29-0.4091-0.61991.73311.13862.7109-0.0115-0.6770.03480.220.071-0.13580.18630.0698-0.0595-0.1877-0.028-0.0140.027-0.0377-0.1983-27.7825.3697-0.6411
3-0.10760.0777-0.32710.13340.58641.35080.00690.02020.0549-0.0373-0.024-0.0611-0.11520.02150.0171-0.0667-0.01910.06220.0309-0.02360.0613-24.228837.9209-15.4795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|154 - A|190 }
2X-RAY DIFFRACTION2{ A|251 - A|452 }
3X-RAY DIFFRACTION3{ A|687 - A|696 }

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