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- PDB-7zfg: VDR complex with aromatic D-ring analog -

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Basic information

Entry
Database: PDB / ID: 7zfg
TitleVDR complex with aromatic D-ring analog
Components
  • Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / complex / agonist / vitamin D receptor
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / vitamin D binding / calcitriol 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 / 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 / estrous cycle / cellular response to Thyroglobulin triiodothyronine / 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 / cerebellum development / 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 estrogen receptor binding / nuclear receptor binding / hippocampus development / 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 / male gonad development / nuclear receptor activity / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / cell differentiation / transcription coactivator activity / 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 / 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. / Nuclear receptor coactivator, interlocking / 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-IV5 / 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: 2.62 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE17-0009-01 France
CitationJournal: J.Med.Chem. / Year: 2022
Title: Design, Synthesis, Biological Activity, and Structural Analysis of Novel Des-C-Ring and Aromatic-D-Ring Analogues of 1 alpha ,25-Dihydroxyvitamin D 3.
Authors: Seoane, S. / Gogoi, P. / Zarate-Ruiz, A. / Peluso-Iltis, C. / Peters, S. / Guiberteau, T. / Maestro, M.A. / Perez-Fernandez, R. / Rochel, N. / Mourino, A.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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)36,3954
Polymers35,8372
Non-polymers5582
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.830, 65.830, 264.920
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IV5 / (1R,3S,5Z)-4-methylidene-5-[(E)-9-methyl-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]-9-oxidanyl-dec-2-enylidene]cyclohexane-1,3-diol


Mass: 498.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H50O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: NaAcetate 2.5M, BisTris 0.1M

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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 9, 2021
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.62→47.9 Å / Num. obs: 11022 / % possible obs: 99.39 % / Redundancy: 2 % / Biso Wilson estimate: 66.28 Å2 / CC1/2: 1 / Net I/σ(I): 35.55
Reflection shellResolution: 2.62→2.71 Å / Num. unique obs: 1045 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2.62→47.9 Å / SU ML: 0.3385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2605 1097 10 %
Rwork0.1986 9874 -
obs0.2048 10971 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.88 Å2
Refinement stepCycle: LAST / Resolution: 2.62→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 40 38 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072073
X-RAY DIFFRACTIONf_angle_d1.00452793
X-RAY DIFFRACTIONf_chiral_restr0.0517311
X-RAY DIFFRACTIONf_plane_restr0.0069352
X-RAY DIFFRACTIONf_dihedral_angle_d24.2629795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.740.34081290.25691157X-RAY DIFFRACTION96.84
2.74-2.880.30011320.24011191X-RAY DIFFRACTION99.85
2.88-3.070.34921330.22681199X-RAY DIFFRACTION99.78
3.07-3.30.31311350.21461219X-RAY DIFFRACTION99.71
3.3-3.630.25021350.2091215X-RAY DIFFRACTION99.48
3.63-4.160.23881380.17791237X-RAY DIFFRACTION99.85
4.16-5.240.22871400.16791263X-RAY DIFFRACTION99.79
5.24-47.90.25911550.20731393X-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)
17.19423011289-2.91638302651-2.537113940975.6991955728-0.7175958341822.456443654880.0267377225238-0.5416059239491.227311339890.28350045729-0.337165559433-0.34914582543-1.42777911387-0.3230824183730.1862192994340.770079017121-0.1456374156950.0535705465560.832898343096-0.1611361424650.856665760381-38.891181299439.32000789967.53899498839
27.49231205831-1.09117649468-2.302274345234.584550152923.966982653689.372207016360.111575556351-0.0550085636103-0.0590724271025-0.296076588295-0.6931468607731.1283498961-0.224264254202-0.774555707920.5923154823650.46119370705-0.03392839785780.0321136500170.525446817054-0.03114199852620.501699442372-32.837595951625.7331172532-10.4636084468
37.191075839082.16519029342-3.179793606454.58602453734-2.73242250288.174023702660.426202686451-1.49186738689-0.03852254004060.893475233481-0.761428375180.9144447259130.5094919075370.4142066789640.3707802406160.716535814782-0.1101292222580.1040302164930.70121914355-0.06595379214190.634658559327-29.545711303223.684542167-1.89294834883
44.83319980435-2.030487480312.724088990368.87973695154-3.687950922114.991415649921.037634594020.554760972501-1.169863425680.683505841241-0.3470413296940.7828729439942.05673373367-1.23815864695-0.446567458431.31532541126-0.233732309428-0.01542820682881.01690988303-0.0273715880530.695838144495-31.45684579639.61885525497-8.81290329893
55.43746733454-1.01444664283-3.042088208945.309796074090.9473016535165.204780222490.0440838242879-0.916925476980.3143182190670.6260871494630.175445378508-0.1429998135680.01331550118070.570688152191-0.1548177194840.695923625419-0.155019800598-0.02281859672220.84999030214-0.06624753844440.464053959143-28.416251879329.32977949028.6583600214
66.75462879908-1.62023249038-4.277989499973.384537155830.8386580753412.702950451490.069033335182-0.6122625057270.02625717051820.4322128610490.163414637581-0.4187385294590.3087833916511.40786369304-0.2691000804290.619899970486-0.040092796626-0.05761953745670.6143836495770.008954010784680.597770911868-19.803265341821.6590580829-5.6486637221
76.351013923872.52932504244-3.630336203692.710540480911.482719031297.107088375431.25186025607-0.3810914291350.163854399022-1.01033232062-0.423835765393-0.726687399805-2.616184384081.73829275284-0.3760859634310.804111131236-0.06465529389590.1737374866820.630424035531-0.09093973113870.948862591667-23.261171949638.0004116847-15.6889292176
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 283 )AA175 - 28322 - 69
33chain 'A' and (resid 284 through 316 )AA284 - 31670 - 102
44chain 'A' and (resid 317 through 334 )AA317 - 334103 - 120
55chain 'A' and (resid 335 through 404 )AA335 - 404121 - 190
66chain 'A' and (resid 405 through 451 )AA405 - 451191 - 237
77chain 'B' and (resid 686 through 695 )BD686 - 6951 - 10

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