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- PDB-8pwf: crystal structure of VDR in complex with Des-C-Ring and Aromatic-... -

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Basic information

Entry
Database: PDB / ID: 8pwf
Titlecrystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 2
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / nuclear receptor / VDR / agonist
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / hematopoietic stem cell proliferation / locomotor rhythm / heart looping ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / hematopoietic stem cell proliferation / locomotor rhythm / heart looping / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / transcription regulator inhibitor activity / cellular response to hormone stimulus / calcium ion homeostasis / Recycling of bile acids and salts / intracellular receptor signaling pathway / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / ossification / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 ...Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / 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
: / Nuclear receptor coactivator 2 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsrochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: J.Med.Chem. / Year: 2023
Title: Further Studies on the Highly Active Des-C-Ring and Aromatic-D-Ring Analogues of 1 alpha ,25-Dihydroxyvitamin D 3 (Calcitriol): Refinement of the Side Chain.
Authors: Zarate-Ruiz, A. / Seoane, S. / Peluso-Iltis, C. / Peters, S. / Gregorio, C. / Guiberteau, T. / Maestro, M. / Perez-Fernandez, R. / Rochel, N. / Mourino, A.
History
DepositionJul 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year / _pdbx_entry_details.has_protein_modification

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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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1473
Polymers35,6412
Non-polymers5071
Water73941
1
A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules

A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2946
Polymers71,2814
Non-polymers1,0132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area3810 Å2
ΔGint-36 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.599, 65.599, 264.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
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: 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 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-FVB / (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)heptyl]phenyl]pent-2-enylidene]cyclohexane-1,3-diol


Mass: 506.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32F6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: LiSO4 1.6M, Hepes 0.1M pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→47.74 Å / Num. obs: 15928 / % possible obs: 98.81 % / Redundancy: 20 % / Biso Wilson estimate: 67.86 Å2 / CC1/2: 1 / Net I/σ(I): 19.28
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 1537 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.74 Å / SU ML: 0.4201 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2651 995 6.29 %
Rwork0.2056 14815 -
obs0.2094 15810 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 35 41 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712085
X-RAY DIFFRACTIONf_angle_d0.85852817
X-RAY DIFFRACTIONf_chiral_restr0.0466313
X-RAY DIFFRACTIONf_plane_restr0.0076363
X-RAY DIFFRACTIONf_dihedral_angle_d16.7824810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.5021380.41512051X-RAY DIFFRACTION98.6
2.42-2.570.39661370.34282024X-RAY DIFFRACTION98.86
2.57-2.770.34331380.29162060X-RAY DIFFRACTION98.96
2.77-3.050.38681390.27862079X-RAY DIFFRACTION99.42
3.05-3.490.33711420.22992101X-RAY DIFFRACTION99.56
3.49-4.40.24011440.18312166X-RAY DIFFRACTION99.35
4.4-47.740.21781570.17252334X-RAY DIFFRACTION99.76
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)
14.40998630001-1.91177590868-2.756273349026.984846712331.523615067376.944114938760.3996603394930.08391173186361.163819470060.429604139346-0.4045365588240.520853305933-0.629925514624-1.360786469210.1402796937270.801401215792-0.08436393365590.1352014421481.32692315823-0.2431821353760.775898473008-38.077666039538.89563373137.81948684357
22.571044068352.643019752571.696919942145.357351452864.657260514.409984923490.05303151140240.1933533915560.384614169098-0.442421901219-1.005044746320.9107741247120.124470600366-1.318736589651.20175955890.787690319091-0.1709795106420.05758041811771.08316569065-0.1589919810440.675538511156-35.169532482516.856702481-13.7252859741
35.932589713051.56810719637-3.174751454575.397484269491.063789866528.361056317590.429115303026-0.5559428654070.4643196042220.0668484338349-0.491081526330.253565476827-0.4067720270240.1113153243570.04270069072730.645262644029-0.001573668792340.004427780186350.772119714482-0.08333968868160.463348398849-27.098003625530.5627942774-5.69208694829
45.62860938939-0.874343058093-2.637594198776.122151592081.223441771618.47217963981-0.7157154138770.0463398132108-1.137302535050.105468803195-0.07799282685410.6895573484761.79450474575-1.377069072970.7810976105811.26578453737-0.3249026258380.2207375232941.02761384948-0.03890141277630.779942068093-32.868224752910.6209429888-5.08643702087
52.472345930980.387472458124-2.613761369855.226073067821.78675663157.12509569134-0.472116600308-0.184436961586-0.2825794856790.9204900776330.1597872192020.1326283302050.70026368117-0.2028602641670.278551620670.821875523257-0.08214341237140.005646501101420.9949637082070.007870730443050.500345638327-29.471151662321.44004531365.99397055128
64.94410871366-0.0143015252074-3.057029293964.554401586681.312393910668.810424636350.448718246312-0.6964524708051.850158415091.7406000905-0.148865375551-0.0744127625556-1.552498772311.89341660006-0.5431620047041.01364088452-0.242913014423-0.05145385451741.28389225148-0.1931653682220.790818991614-14.641618699936.76104545062.57012893706
76.91713170784-1.67881134278-1.934444607464.99270076681.538694307972.948376351390.404944197796-2.108753445010.5461335961581.49279731121-0.204827505360.00417977508082-0.8823500711420.87817589008-0.4051031256261.16280778205-0.2071361597220.1271645838141.58182927061-0.2727272662440.706349841838-29.706136670936.084245311513.8952435746
85.62994436028-2.06486577082-2.371235143514.688154949472.503012983542.94094141721-0.577765652166-1.88906552954-0.01430689528581.098896156530.400526389935-0.01240784244540.9716470268061.532384700950.1089759077780.9885188081960.0999558193877-0.04582030185891.13563350157-0.04372354376230.526077467944-20.840354762621.59315199114.2642482714
98.73824589227-3.53858802777-3.108508999088.293843567935.762236492028.42035937252-0.2938192434310.280869354518-0.04853789008381.399463574560.437865849338-0.4690420690811.91042249641.41427107901-0.06742117058010.9209348284550.09825660947580.01856117230380.9048633724910.06206820677080.46418193847-18.152003401222.073862902-17.0748604921
103.255281378980.5171039790792.560162668133.31256979514-1.798775935223.634074531480.6613877832361.464688619851.43850252864-0.0547489756904-0.544918027688-0.0336177424371-1.820413518031.26032536924-0.18584683071.08690615077-0.125154043470.04515450662810.843831783911-0.03550571613620.819494976865-24.017123528638.1548891699-14.9574433048
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 154 through 174 )AA154 - 1741 - 21
22chain 'A' and (resid 175 through 254 )AA175 - 25422 - 41
33chain 'A' and (resid 255 through 305 )AA255 - 30542 - 92
44chain 'A' and (resid 306 through 334 )AA306 - 33493 - 121
55chain 'A' and (resid 335 through 367 )AA335 - 367122 - 154
66chain 'A' and (resid 368 through 378 )AA368 - 378155 - 165
77chain 'A' and (resid 379 through 401 )AA379 - 401166 - 188
88chain 'A' and (resid 402 through 431 )AA402 - 431189 - 218
99chain 'A' and (resid 432 through 451 )AA432 - 451219 - 238
1010chain 'B' and (resid 687 through 695 )BB687 - 6951 - 9

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