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- PDB-9eyr: VDR complex with gemini analog UG-480 -

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Basic information

Entry
Database: PDB / ID: 9eyr
TitleVDR complex with gemini analog UG-480
Components
  • Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / agonist / vitamin D receptor complex
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 receptor 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 receptor 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 / hippocampus development / nuclear estrogen receptor binding / 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 / regulation of DNA-templated transcription / chromatin / 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 / cytoplasm / cytosol
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
: / 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: 2.56 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: J.Med.Chem. / Year: 2024
Title: Design, Synthesis, and Biological Evaluation of New Type of Gemini Analogues with a Cyclopropane Moiety in Their Side Chain.
Authors: Gomez-Bouzo, U. / Peluso-Iltis, C. / Santalla, H. / Quevedo, M.A. / Verlinden, L. / Verstuyf, A. / Fall, Y. / Gomez, G. / Rochel, N.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3663
Polymers35,8372
Non-polymers5291
Water55831
1
A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 1
hetero molecules

A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 1
hetero molecules


  • defined by software
  • Evidence: gel filtration
  • 72.7 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)72,7316
Polymers71,6734
Non-polymers1,0582
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area4120 Å2
ΔGint-27 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.670, 65.670, 263.730
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 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-A1H75 / (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{R})-5-methyl-1-[(1~{S},2~{S})-2-(3-methyl-3-oxidanyl-butyl)cyclopropyl]-5-oxidanyl-hexyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol


Mass: 528.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H56O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Li2SO4 1.8M

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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 PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.56→43.6 Å / Num. obs: 11733 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 68.93 Å2 / CC1/2: 1 / Net I/σ(I): 3.1
Reflection shellResolution: 2.56→2.65 Å / Num. unique obs: 1123 / CC1/2: 0.973

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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: 2.56→43.06 Å / SU ML: 0.2931 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9612
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 1167 9.98 %
Rwork0.2161 10523 -
obs0.2203 11690 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.84 Å2
Refinement stepCycle: LAST / Resolution: 2.56→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 38 31 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222081
X-RAY DIFFRACTIONf_angle_d0.50792812
X-RAY DIFFRACTIONf_chiral_restr0.0363319
X-RAY DIFFRACTIONf_plane_restr0.0053356
X-RAY DIFFRACTIONf_dihedral_angle_d17.6674809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.670.33921390.291251X-RAY DIFFRACTION98.86
2.67-2.810.33261420.25871275X-RAY DIFFRACTION99.51
2.81-2.990.32961450.2861297X-RAY DIFFRACTION99.72
2.99-3.220.3271400.25941265X-RAY DIFFRACTION99.65
3.22-3.540.29611430.22341305X-RAY DIFFRACTION99.72
3.55-4.060.2331440.20561315X-RAY DIFFRACTION99.39
4.06-5.110.21441500.17711344X-RAY DIFFRACTION99.87
5.11-43.060.25331640.21651471X-RAY DIFFRACTION99.88
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)
13.67987885585-1.535620757493.589645589174.17722468052-1.485723494957.859097846340.1753459554060.021551829196-0.1730933059520.341685130089-0.420576649174-0.4010136933810.03745647594690.306150127870.2576342714890.44899722703-0.1042731513370.01867928259040.6280295550750.07692970854630.4288166418831.309826119-29.1480442385-4.45700579712
25.66659921748-0.6640049848091.844085239846.47452637515-0.8264204314817.59418501889-0.3122800881840.0829288587791.54341945612-0.362642115659-0.296540673993-0.463933783832-1.978203814820.5667413581450.8123603515021.4421110031-0.252162314486-0.2585567197680.931249340340.09438639195690.97343899993431.11553714-10.0339610253-4.90170901095
33.3334750638-0.5874437074221.691263618692.59995724297-0.9322279507235.28081371534-0.114031774774-0.7541454174340.02784301842280.634972855924-0.03097424887180.049446950575-0.368772047346-0.4053464417220.1680013007270.657769536462-0.09047826426390.03953452853430.7098012461420.004993331115230.4674655555723.8582332221-26.38302887982.88819354214
48.57963345772.64614393691-0.5254438083397.885192719050.2241829161872.06922503911-0.281025455828-0.162723185361-1.10369770088-0.873591159197-0.285024104010.3187825236821.88631441702-1.202373307710.3556626421430.910361240054-0.0966564071887-0.1280760287860.7711078116490.06495906863750.57385777823322.9807254288-37.6231637931-14.9974496739
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 305 )AA154 - 3051 - 92
22chain 'A' and (resid 306 through 338 )AA306 - 33893 - 125
33chain 'A' and (resid 339 through 452 )AA339 - 452126 - 239
44chain 'B' and (resid 686 through 695 )BC686 - 6951 - 10

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