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- PDB-7bns: VDR complex with BXL-62 -

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Basic information

Entry
Database: PDB / ID: 7bns
TitleVDR complex with BXL-62
Components
  • Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / nuclear receptor / agonist
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element 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 / vitamin D response element 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 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / 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 / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / ossification / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear estrogen receptor binding / hippocampus development / nuclear receptor binding / 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 / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / 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 / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / 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 / 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
1,25-Dihydroxy-16-ene-20-cyclopropyl-vitamin D3 / 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: 2.7 Å
AuthorsRochel, N. / Belorusova, A.Y.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-13-BSV8-0024-01 France
CitationJournal: Int J Mol Sci / Year: 2022
Title: Vitamin D Analogs Bearing C-20 Modifications Stabilize the Agonistic Conformation of Non-Responsive Vitamin D Receptor Variants.
Authors: Belorusova, A.Y. / Rovito, D. / Chebaro, Y. / Doms, S. / Verlinden, L. / Verstuyf, A. / Metzger, D. / Rochel, N. / Laverny, G.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A2: Vitamin D3 receptor A
B2: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2633
Polymers35,8372
Non-polymers4271
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.874, 65.874, 263.683
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A2-4132-

HOH

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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: 34060.672 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 BL21(DE3) (bacteria) / References: UniProt: Q9PTN2
#2: Protein/peptide Nuclear receptor coactivator 1 / / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-U5W / 1,25-Dihydroxy-16-ene-20-cyclopropyl-vitamin D3 / (1R,3S,5Z)-5-[(2E)-2-[(3aS,7aS)-7a-methyl-1-[1-(4-methyl-4-oxidanyl-pentyl)cyclopropyl]-3a,5,6,7-tetrahydro-3H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol


Mass: 426.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H42O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→24.8 Å / Num. obs: 10014 / % possible obs: 98.35 % / Redundancy: 1.3 % / Biso Wilson estimate: 57.68 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.795 Å / Num. unique obs: 928 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hc4

2hc4


Resolution: 2.7→24.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 994 9.97 %
Rwork0.1768 8973 -
obs0.1851 9967 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.91 Å2 / Biso mean: 71.2052 Å2 / Biso min: 30.3 Å2
Refinement stepCycle: final / Resolution: 2.7→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 31 38 2071
Biso mean--57.7 70.77 -
Num. residues----248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.840.32541330.23361198133195
2.84-3.020.35081400.22141256139699
3.02-3.250.30121370.21271233137099
3.25-3.580.29271410.19921266140799
3.58-4.090.23621420.15461294143699
4.09-5.150.21481430.14271300144399
5.15-24.80.25331580.17871426158499
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)
16.1705-0.86311.5427.89313.85272.5-0.1373-0.11281.1442-0.3066-0.3171-0.0586-0.47840.30890.35140.4237-0.00440.0420.747-0.02290.53878.99451.737744.0679
29.0099-2.3815-1.7336.4209-4.90825.3718-0.084-0.3337-0.1341-0.7825-0.05661.31040.0015-0.62380.27310.4727-0.0276-0.10570.747-0.15750.4904-5.72232.356427.1816
34.95330.82770.51555.9973.95058.7161-0.1144-0.59680.3831-0.07340.1356-0.3818-0.26870.0277-0.03470.38310.0367-0.04130.3824-0.01420.326312.146839.942337.968
46.0588-1.0182-0.55897.3613-0.30738.7693-0.0759-0.028-0.40370.1776-0.28271.3893-0.3873-1.80080.40420.4463-0.08930.02110.9562-0.10920.7162-7.693535.23838.9526
52.7431-1.2629-0.42515.6282.87535.4973-0.1712-0.6245-0.24050.73220.08030.06540.42130.14020.07310.58010.0527-0.04050.78130.02290.35977.596436.829648.8946
61.28230.04470.24977.70254.07545.4205-0.1562-0.69260.05221.0740.3002-0.26620.37820.248-0.19380.62870.0632-0.08830.88480.01480.411312.055336.760152.1948
78.0058-4.61240.95263.1272-0.04492.65740.5054-0.2012-0.92140.1149-0.0809-0.29990.34070.1642-0.46720.4053-0.0428-0.05170.6078-0.03990.42069.76927.578527.358
88.7097-3.3510.70928.58562.53052.22910.26740.3078-0.3802-1.65190.3278-0.8860.25942.0373-0.54910.7644-0.00640.03750.8187-0.00720.527820.851339.445328.358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A2' and (resid 155 through 184 )A2155 - 184
2X-RAY DIFFRACTION2chain 'A2' and (resid 185 through 254 )A2185 - 254
3X-RAY DIFFRACTION3chain 'A2' and (resid 255 through 306 )A2255 - 306
4X-RAY DIFFRACTION4chain 'A2' and (resid 307 through 334 )A2307 - 334
5X-RAY DIFFRACTION5chain 'A2' and (resid 335 through 376 )A2335 - 376
6X-RAY DIFFRACTION6chain 'A2' and (resid 377 through 431 )A2377 - 431
7X-RAY DIFFRACTION7chain 'A2' and (resid 432 through 452 )A2432 - 452
8X-RAY DIFFRACTION8chain 'B2' and (resid 687 through 696 )B2687 - 696

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