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- PDB-7b39: Allene-Based Design of a Noncalcemic Vitamin D Receptor Agonist -

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Basic information

Entry
Database: PDB / ID: 7b39
TitleAllene-Based Design of a Noncalcemic Vitamin D Receptor Agonist
Components
  • Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsGENE REGULATION / vitamin d receptor
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 mediated 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 mediated 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 / nuclear estrogen receptor binding / hippocampus development / 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 / chromatin / regulation of DNA-templated transcription / 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 / cytosol / cytoplasm
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
ACETATE ION / Chem-T0H / 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: 2.13 Å
AuthorsRochel, N.
CitationJournal: Chemistry / Year: 2021
Title: Design, Synthesis, Evaluation and Structure of Allenic 1 alpha ,25-Dihydroxyvitamin D 3 Analogs with Locked Mobility at C-17.
Authors: Fraga, R. / Len, K. / Lutzing, R. / Laverny, G. / Loureiro, J. / Maestro, M.A. / Rochel, N. / Rodriguez-Borges, E. / Mourino, A.
History
DepositionNov 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,3084
Polymers35,8372
Non-polymers4722
Water1,26170
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


Theoretical massNumber of molelcules
Total (without water)72,6178
Polymers71,6734
Non-polymers9434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4700 Å2
ΔGint-35 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 66.250, 264.390
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-T0H / (1R,3S,Z)-5-(2-((3aS,7aS,E)-1-(6-hydroxy-6-methylhept-1-en-1-ylidene)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-4-methylenecyclohexane-1,3-diol / (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-(6-methyl-6-oxidanyl-hept-1-enylidene)-2,3,3~{a},5,6,7-hexahydroinden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol


Mass: 412.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H40O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.9 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate

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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: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.13→24.9 Å / Num. obs: 20242 / % possible obs: 99.05 % / Redundancy: 2 % / Biso Wilson estimate: 52.35 Å2 / CC1/2: 1 / Net I/σ(I): 33.05
Reflection shellResolution: 2.13→2.206 Å / Num. unique obs: 1921 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2.13→24.9 Å / SU ML: 0.2512 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 1980 9.82 %
Rwork0.2013 18179 -
obs0.2058 20159 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.69 Å2
Refinement stepCycle: LAST / Resolution: 2.13→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 34 70 2131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222130
X-RAY DIFFRACTIONf_angle_d0.45472879
X-RAY DIFFRACTIONf_chiral_restr0.0354323
X-RAY DIFFRACTIONf_plane_restr0.0039373
X-RAY DIFFRACTIONf_dihedral_angle_d18.1973829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.34821310.31511204X-RAY DIFFRACTION96.46
2.18-2.240.36531370.29041258X-RAY DIFFRACTION97.89
2.24-2.30.33151360.27581255X-RAY DIFFRACTION98.17
2.3-2.380.32641370.251258X-RAY DIFFRACTION98.66
2.38-2.460.31761370.25661265X-RAY DIFFRACTION98.66
2.46-2.560.3071370.24161261X-RAY DIFFRACTION98.45
2.56-2.680.3671390.24381269X-RAY DIFFRACTION99.02
2.68-2.820.29821400.23891287X-RAY DIFFRACTION99.58
2.82-30.26471430.24411309X-RAY DIFFRACTION99.93
3-3.230.25671420.24091299X-RAY DIFFRACTION99.79
3.23-3.550.28541420.22261312X-RAY DIFFRACTION99.73
3.55-4.060.21671480.18351346X-RAY DIFFRACTION99.8
4.06-5.110.20971490.15611372X-RAY DIFFRACTION99.93
5.12-24.90.2151620.17781484X-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)
13.65579882494-1.88589206524-2.253146939066.292596687624.65153346229.335196556320.138888616318-0.8764852024511.105942653940.364113919927-0.167375697380.143577161715-1.21382341172-0.02678922689740.1354909929910.595244373597-0.08506940688880.08001538817050.765497437802-0.282353300820.703343239849-39.509854183839.87140165417.10138313687
22.17087075564-2.98357130133-2.784656443494.113038153043.94656695264.630380518450.6230966125390.243158895274-0.418536001657-0.319680950815-1.600943434081.82334235712-0.96390883174-1.915017565990.8236288907770.542430170735-0.1225896396120.1053410537990.86143413429-0.1758664454860.649819660658-41.921693491323.3546208979-10.9627235752
31.96751447367-0.5949896550071.405534800849.557249905151.683311809257.778582796420.308625281490.333173355149-1.104894841840.340205749517-0.5215456004320.3474581974380.7908204682990.1323281860510.2376394428860.598750481894-0.06820977890750.05153761375230.580622673463-0.09631387190750.587954946546-30.923703206711.4005872738-16.7474948243
44.051296399880.92681040383-1.642004311675.679544814412.727031951188.463496894250.26863363169-0.3837040654950.376355861480.187735608985-0.00992433116109-0.055052071175-0.3583998732870.409433786011-0.2523644179530.326926357465-0.0547696308410.03469908982550.479583957864-0.07597100237130.370679662674-28.3974183130.8747986099-5.97537494446
54.88855708691-1.32946845403-1.508573836493.667113645022.403419641062.80895924851-0.261235479544-0.414541389683-0.6208023474970.35175168406-0.1306147498620.3767687660821.37046050056-0.553133777360.4615398334950.915383848231-0.11498022080.1393589772640.6456358654230.07280360852860.586137742902-32.277893653812.3431555854-1.31365578229
68.34178067146-0.286404303396-3.78093683754.294235402660.6894509980387.83941277008-0.0481699273789-0.8478664870130.758323005813-0.007372070764640.341643896234-0.145600651862-0.1205340101630.978071158782-0.2004631804460.583178987403-0.139839274899-0.01031407291110.80179025872-0.1562175069040.379780331647-28.295493656432.37506469065.03324636237
78.639147435781.32891678728-3.893636193056.031862922570.5395143404397.797627837670.42701640637-2.02443746930.835849852060.692577533944-0.16732092892-0.0551869290351-0.7743562452721.40496165759-0.09229096008520.758204229049-0.200606493997-0.002451404966361.14034857776-0.2763574018790.557893726005-30.077299160237.317810638812.8978395309
87.99165146392-3.08254595427-5.763259111584.015725424433.257923762454.5532541277-0.175932739112-2.18880649768-0.2320758307420.7443839765610.387143265475-0.05505635136480.1594182686131.9576312481-0.235685107480.5902900305270.00734025270579-0.09970340381650.861902436508-0.003968095956580.467378480069-22.197671159221.95181644934.20847084579
99.06787674552-2.86367627717-2.464612248768.844188076982.572132675365.32823259895-0.0677223373974-0.189389557052-0.01497818973550.5693484224360.310731065222-0.8075941837210.3901466433540.74240853447-0.2565353172070.6104405458120.0444913931844-0.01436422159360.5787286102-0.0536556626920.43771323628-18.757553297822.9647957009-16.3886893691
102.88595253697-4.53133792799-1.688804314567.509978235923.567374643974.76255709633-0.1328497721080.4156538077110.791833573947-0.284442017860.2473459457040.453699446728-1.489006062660.97619272661-0.1529709567820.85265639574-0.05244591073530.07296451129620.668418132261-0.03951863202940.738944095415-24.501653843838.5792321565-15.4968317041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 154 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 254 )
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 305 )
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 351 )
6X-RAY DIFFRACTION6chain 'A' and (resid 352 through 376 )
7X-RAY DIFFRACTION7chain 'A' and (resid 377 through 401 )
8X-RAY DIFFRACTION8chain 'A' and (resid 402 through 431 )
9X-RAY DIFFRACTION9chain 'A' and (resid 432 through 453 )
10X-RAY DIFFRACTION10chain 'B' and (resid 686 through 696 )

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