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

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Basic information

Entry
Database: PDB / ID: 7bnu
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: 2.4 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)36,2883
Polymers35,8622
Non-polymers4271
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-8 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.658, 65.658, 264.139
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

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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: 34085.660 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.: 69 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
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: ID23-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.77 Å / Num. obs: 15931 / % possible obs: 99.21 % / Redundancy: 2 % / Biso Wilson estimate: 49.97 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 1538 / CC1/2: 0.98

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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: 2.4→29.4 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 677 4.84 %
Rwork0.1886 13320 -
obs0.1923 13997 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.52 Å2 / Biso mean: 74.0238 Å2 / Biso min: 35.81 Å2
Refinement stepCycle: final / Resolution: 2.4→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 31 69 2082
Biso mean--57.7 74.69 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.580.33471220.24392566268898
2.59-2.850.2931110.21212630274199
2.85-3.260.30071360.206126122748100
3.26-4.10.24751450.175826832828100
4.1-29.40.24611630.17932829299299
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)
12.19571.5771-2.45041.8758-0.10928.66040.22380.0501-1.7518-0.5802-0.456-0.10381.4456-0.96060.08380.8814-0.1212-0.08670.68630.06140.5724.5664-38.1544-15.4592
23.237-0.78022.80283.4391-2.01356.66920.0941-0.2399-0.35640.1919-0.1465-0.33270.14580.23870.08960.4154-0.0749-0.0270.59820.06770.407232.519-29.7785-5.0088
38.96463.47565.44051.39322.12563.3131-0.0326-0.74441.2885-0.1812-0.1159-0.6973-1.62460.48660.71911.0132-0.2498-0.1970.893-0.08480.71636.977-12.12731.0058
43.4608-0.91752.06933.5026-0.83967.18230.0126-0.9040.0130.4913-0.0927-0.0394-0.3833-0.29840.0970.6074-0.1077-0.01390.90560.0230.446629.1863-25.3714.9613
53.8431-1.20992.25723.3327-2.35582.5524-0.0322-0.83440.1170.42730.29990.4152-0.217-0.9703-0.22260.5473-0.02510.05770.72990.03960.45319.682-21.9084-5.7181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B2' and (resid 687 through 695 )B2687 - 695
2X-RAY DIFFRACTION2chain 'A2' and (resid 155 through 305 )A2155 - 305
3X-RAY DIFFRACTION3chain 'A2' and (resid 306 through 315 )A2306 - 315
4X-RAY DIFFRACTION4chain 'A2' and (resid 316 through 404 )A2316 - 404
5X-RAY DIFFRACTION5chain 'A2' and (resid 405 through 452 )A2405 - 452

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