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- PDB-9ez1: Vitamin D receptor in complex with 1,4a,25-trihydroxyvitamin D3 -

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Basic information

Entry
Database: PDB / ID: 9ez1
TitleVitamin D receptor in complex with 1,4a,25-trihydroxyvitamin D3
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / agonist / vitamin D metabolites / VDR
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 / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / 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 / protein dimerization activity / nuclear body / 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: 1.95 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Biomolecules / Year: 2024
Title: 4-Hydroxy-1 alpha ,25-Dihydroxyvitamin D 3 : Synthesis and Structure-Function Study.
Authors: Peluso-Iltis, C. / Pierrat, N. / Rovito, D. / Osz, J. / Sawada, D. / Kittaka, A. / Laverny, G. / Rochel, N.
History
DepositionApr 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 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)36,1304
Polymers35,6412
Non-polymers4902
Water1,44180
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


  • defined by software
  • Evidence: gel filtration
  • 72.3 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)72,2608
Polymers71,2814
Non-polymers9794
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4630 Å2
ΔGint-35 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.980, 65.980, 263.470
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
Components on special symmetry positions
IDModelComponents
11A-670-

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 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-A1H9P / 1,4a,25-trihydroxyvitamin D3 / (1S,2S,4S,6E)-6-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(E,2R)-6-methyl-6-oxidanyl-hept-4-en-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-5-methylidene-cyclohexane-1,2,4-triol


Mass: 430.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0,2.5 M NaOAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→43.91 Å / Num. obs: 25896 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 43.55 Å2 / CC1/2: 1 / Net I/σ(I): 22.96
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 2487 / CC1/2: 0.948

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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: 1.95→43.91 Å / SU ML: 0.2658 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.0197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 1992 7.73 %
Rwork0.2084 23783 -
obs0.2122 25775 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 35 80 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882101
X-RAY DIFFRACTIONf_angle_d1.00752840
X-RAY DIFFRACTIONf_chiral_restr0.055322
X-RAY DIFFRACTIONf_plane_restr0.0094363
X-RAY DIFFRACTIONf_dihedral_angle_d15.7112814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.36721330.38391586X-RAY DIFFRACTION95.02
2-2.050.36661390.3131648X-RAY DIFFRACTION99.11
2.05-2.110.34151380.27631642X-RAY DIFFRACTION98.78
2.11-2.180.27851390.26241654X-RAY DIFFRACTION99.12
2.18-2.260.30781390.24931652X-RAY DIFFRACTION99.22
2.26-2.350.29731400.23421671X-RAY DIFFRACTION99.29
2.35-2.450.32321410.23251681X-RAY DIFFRACTION99.35
2.45-2.580.28651390.2341670X-RAY DIFFRACTION99.12
2.58-2.740.3351420.24671703X-RAY DIFFRACTION99.35
2.74-2.960.29651420.2521695X-RAY DIFFRACTION99.67
2.96-3.250.33381440.24381714X-RAY DIFFRACTION99.68
3.25-3.720.24711450.19681749X-RAY DIFFRACTION99.58
3.72-4.690.1981490.16461780X-RAY DIFFRACTION99.9
4.69-43.910.2241620.1851938X-RAY DIFFRACTION99.9
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)
12.39002796358-2.73886857485-0.5016419643854.47978570525-1.07396400792.057776741280.227542468462-0.3452174143131.16017045855-0.124603256276-0.484245496312-0.0927800202292-0.85834864886-0.1515528490510.2280270247310.602301836952-0.09554439899490.04791507382620.74392356188-0.244046734020.613846841557-39.879162816239.96579538597.24081310324
23.33921593237-2.00091681272-2.595764192962.041839535271.925209884562.190206953160.1275677854340.02620655810550.155423944356-0.334794045712-0.8999019178380.870348766366-0.224022433682-2.248860507220.7692393243920.54841061964-0.08431598303780.01127679506480.857005415286-0.1880770938430.516205107789-42.298434186523.1553199125-10.9462384554
35.90841630455-3.141277116034.33853321528.29158614838-0.02261802476554.484637661890.2554565863370.255388096756-0.2878492088410.596967715848-0.3913639655510.6832579960670.5100429980530.313301313980.04625156129550.622239833946-0.07192135707760.04332015841480.550935278196-0.05347717450410.371122877871-32.789829064911.9067649615-16.4633975187
45.34995036326-2.01294335841-1.761730080492.749620713310.5542392022826.609791283520.161517074795-0.3600364069670.1146903751230.237328946559-0.1887359724590.1531000425070.116528898995-0.1776752682370.01976144630360.401760288944-0.05393646078490.04152464002530.461680067851-0.05581529031680.23762947008-30.886114858427.0900889698-4.92795266238
53.50852406064-1.14726090747-2.172763065872.813386352432.184776742235.75024858051-0.111819788737-0.7908161515560.06146840317890.4063606783430.180898655553-0.0347301639530.3833249294090.499707112188-0.03765389517680.561298367676-0.0339070136846-0.02823599124510.710306269653-0.004186882036050.29680553471-27.795720061124.65904768144.33359183492
65.981339672111.008382731521.394027700673.180834970695.126399191518.38352720799-0.003709557493010.270492765159-0.2151012664450.6579174480830.415798089026-0.8388564078850.2743011924880.794200684208-0.3422329211810.5216616562570.0166347228461-0.0140284309440.480435410039-0.03162982726950.331458541073-19.734093590622.9889066695-16.3701913983
74.954947708722.67506437986-0.1314918470264.50018138296-0.07987766875894.427973608990.2285162011070.5177658274030.43690042267-0.593033569744-0.0300718680982-0.204298105512-1.192435179580.942639301624-0.1415217047320.733295889172-0.05670012273850.04521804817650.634612395499-0.05988186538060.45729311392-24.417898835137.5929190117-15.7498982543
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 184 )AA175 - 18422 - 31
33chain 'A' and (resid 185 through 254 )AA185 - 25432 - 40
44chain 'A' and (resid 255 through 318 )AA255 - 31841 - 104
55chain 'A' and (resid 319 through 432 )AA319 - 432105 - 218
66chain 'A' and (resid 433 through 453 )AA433 - 453219 - 239
77chain 'B' and (resid 686 through 695 )BB686 - 6951 - 10

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