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- PDB-9ez2: Vitamin D receptor complex with 1,4b,25-trihydroxyvitamin D3 -

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Basic information

Entry
Database: PDB / ID: 9ez2
TitleVitamin D receptor complex with 1,4b,25-trihydroxyvitamin D3
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / agonist / vitamin D metabolite / VDR
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 / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element 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 / 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 / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / 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 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
: / 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: 1.8 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)36,1324
Polymers35,6412
Non-polymers4922
Water2,216123
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)72,2648
Polymers71,2814
Non-polymers9834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4640 Å2
ΔGint-35 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.140, 66.140, 263.740
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-704-

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-A1H72 / 1,4b,25-trihydroxyvitamin D3 / (1R,2S,4S,6E)-6-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-5-methylidene-cyclohexane-1,2,4-triol


Mass: 432.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O4 / 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.: 123 / 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: 47.35 %
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: 1.8→47.99 Å / Num. obs: 32871 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 41.22 Å2 / CC1/2: 1 / Net I/σ(I): 23.45
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3184 / CC1/2: 0.915

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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: 1.8→47.99 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1985 6.07 %
Rwork0.2018 30703 -
obs0.2035 32688 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 35 123 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612121
X-RAY DIFFRACTIONf_angle_d0.7852868
X-RAY DIFFRACTIONf_chiral_restr0.0476325
X-RAY DIFFRACTIONf_plane_restr0.0075367
X-RAY DIFFRACTIONf_dihedral_angle_d14.5367824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.49841350.48692097X-RAY DIFFRACTION97.25
1.84-1.890.39061350.39832107X-RAY DIFFRACTION98.38
1.89-1.950.39331390.32942134X-RAY DIFFRACTION99.04
1.95-2.010.29311380.27372131X-RAY DIFFRACTION98.65
2.01-2.080.25261390.23172129X-RAY DIFFRACTION98.91
2.08-2.170.25231380.22672154X-RAY DIFFRACTION99.31
2.17-2.270.27741370.23152161X-RAY DIFFRACTION99.31
2.27-2.390.29091410.21992177X-RAY DIFFRACTION99.4
2.39-2.540.22521430.20992191X-RAY DIFFRACTION99.66
2.54-2.730.22651430.21922198X-RAY DIFFRACTION99.7
2.73-3.010.2771430.22952224X-RAY DIFFRACTION99.83
3.01-3.440.20541450.20842228X-RAY DIFFRACTION99.87
3.44-4.330.20031490.16342293X-RAY DIFFRACTION99.92
4.34-47.990.20811600.18012479X-RAY DIFFRACTION99.92
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)
19.805209469771.643058264062.781259527136.162850165354.649880228353.826188516970.0499183369025-0.0328463641416-0.2532545832420.2530277555070.257341766393-0.6200031589950.1718177341160.735502257723-0.3715036823850.5140872466210.01724084857780.03475567753320.474789193677-0.01223130010950.292563607815-19.133593743622.7940635367-16.2927639098
23.379918536620.03320678074713.123808136730.400730384145-0.01387358173772.95324757575-0.07829206736420.5346843782090.659788223942-0.1787318827-0.08180119376390.00162991541133-1.248929611930.5598446850820.06048921587030.567428389040.004185512654630.06984241592480.452234034701-0.02797271649440.444038202581-24.242723960737.737392538-15.6864503165
33.7914544635-0.873125719693-2.03147348742.223414187412.037213243926.316570695290.135775204314-0.2193800080.1817919709880.049478406483-0.2229085411860.1763575887440.0891237193877-0.3523520316110.06893557020160.307051266199-0.06384573997340.01051725022650.380912435662-0.04493668773760.26637556307-33.85783671727.8848546636-4.23736997504
43.33883656705-1.91875270921-2.73262158663.153469953412.210803871895.70621030707-0.0546828438859-0.671534189698-0.01428836066670.4373799691520.07715365285890.01022226181320.3730721501250.405572778886-0.005300117639840.451442073071-0.0682075188622-0.02915490003560.572566813872-0.01171442378850.292623118615-28.047073630924.69436800214.446809565
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 432 through 453 )AA432 - 453219 - 240
22chain 'B' and (resid 686 through 695 )BC686 - 6951 - 10
33chain 'A' and (resid 154 through 316 )AA154 - 3161 - 103
44chain 'A' and (resid 317 through 431 )AA317 - 431104 - 218

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