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

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Basic information

Entry
Database: PDB / ID: 8pwm
TitleCrystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 3b
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 / calcitriol binding / vitamin D binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / locomotor rhythm ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / calcium ion homeostasis / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ossification / 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 receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / nuclear body / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific 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 / 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 / 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
ACETATE ION / : / 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: To Be Published
Title: Novel Des-C-Ring and Aromatic-D-Ring analogs Acting as Potent Agonists of the Vitamin D Receptor (VDR)
Authors: Rochel, N.
History
DepositionJul 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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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)36,1884
Polymers35,6412
Non-polymers5482
Water84747
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)72,3768
Polymers71,2814
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4730 Å2
ΔGint-31 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.849, 65.849, 264.213
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: 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HXI / (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)hept-3-ynyl]phenyl]but-2-enylidene]cyclohexane-1,3-diol


Mass: 488.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26F6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NaAcetate 2.5M, BisTris 0.1M pH 7

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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→25 Å / Num. obs: 16042 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1566 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.81 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 1598 10.01 %
Rwork0.1955 --
obs0.2013 15957 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 38 47 2085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d1.063
X-RAY DIFFRACTIONf_dihedral_angle_d17.133817
X-RAY DIFFRACTIONf_chiral_restr0.051318
X-RAY DIFFRACTIONf_plane_restr0.007371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.55041410.48871275X-RAY DIFFRACTION99
2.37-2.460.4411400.42781255X-RAY DIFFRACTION99
2.46-2.560.39241400.34021259X-RAY DIFFRACTION99
2.56-2.670.30651400.27221259X-RAY DIFFRACTION100
2.67-2.810.32371420.24991273X-RAY DIFFRACTION99
2.81-2.990.34011460.23471309X-RAY DIFFRACTION100
2.99-3.220.33851420.2261272X-RAY DIFFRACTION100
3.22-3.540.26781460.19111311X-RAY DIFFRACTION99
3.54-4.050.23771470.16231323X-RAY DIFFRACTION100
4.06-5.10.18991510.14771347X-RAY DIFFRACTION100
5.1-24.810.21591630.17751476X-RAY DIFFRACTION100
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)
15.0095-1.6489-2.08155.32195.10384.91870.1602-0.07660.318-0.5967-1.40661.1268-0.9029-1.7561.11340.7529-0.13750.04020.8734-0.10330.7343-40.367933.67240.1099
26.85631.36763.79374.1162-3.28496.34910.21360.1981-0.5340.2051-0.29450.14960.33170.25380.07250.9088-0.05450.10410.9018-0.14720.6764-31.420411.0115-16.8641
35.8569-1.5448-3.47362.91.30557.03650.4125-0.52730.48260.091-0.44350.0167-0.2654-0.11240.02490.6768-0.09380.00220.6523-0.08990.4542-28.627830.4869-5.8614
44.6171-2.1143-1.13395.4411.26417.9888-0.6227-0.2844-0.8305-0.0973-0.19750.37571.9869-0.97250.7461.3043-0.27720.20630.89840.03220.9059-34.50210.847-4.9561
54.18080.2639-3.30612.88860.63785.0785-0.0279-0.6138-0.08420.6646-0.10.29960.43480.14760.23370.9438-0.0747-0.01050.9270.0240.5126-28.222625.17815.0274
64.9159-1.284-1.20041.48881.34515.7373-0.0643-0.96790.18910.51820.21560.09380.09480.6256-0.22890.738-0.1520.01850.5897-0.0270.5444-23.945427.04671.4753
77.30636.34670.39058.1713-0.10452.00150.1504-0.03950.2018-1.29030.3267-0.4028-1.30461.9061-0.56611.1252-0.13820.09811.054-0.12650.6596-23.907237.6733-15.6452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 155 through 184 )
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 254 )
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 306 )
4X-RAY DIFFRACTION4chain 'A' and (resid 307 through 334 )
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 376 )
6X-RAY DIFFRACTION6chain 'A' and (resid 377 through 452 )
7X-RAY DIFFRACTION7chain 'B' and (resid 686 through 695 )

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