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- PDB-8pz8: crystal structure of VDR in complex with D-Bishomo-1a,25-dihydrox... -

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Basic information

Entry
Database: PDB / ID: 8pz8
Titlecrystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 54
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / nuclear receptor / VDR / agonist
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / hematopoietic stem cell proliferation / heart looping / locomotor rhythm ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / hematopoietic stem cell proliferation / heart looping / locomotor rhythm / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cellular response to hormone stimulus / Recycling of bile acids and salts / calcium ion homeostasis / transcription regulator inhibitor activity / intracellular receptor signaling pathway / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / ossification / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / cell differentiation / transcription coactivator activity / 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 / Nuclear receptor coactivators bHLH domain / 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 / Double treble clef zinc finger, C4 type / 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 2 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE17-0009-01 France
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Design, synthesis, and biological activity of D-bishomo-1 alpha ,25-dihydroxyvitamin D 3 analogs and their crystal structures with the vitamin D nuclear receptor.
Authors: Fabisiak, A. / Brzeminski, P. / Sicinski, R.R. / Rochel, N. / Maj, E. / Filip-Psurska, B. / Wietrzyk, J. / Plum, L.A. / DeLuca, H.F.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.oligomeric_count ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

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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)36,0733
Polymers35,6412
Non-polymers4331
Water70339
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


Theoretical massNumber of molelcules
Total (without water)72,1466
Polymers71,2814
Non-polymers8652
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4020 Å2
ΔGint-34 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.370, 65.370, 262.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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-IFU / (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{S},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,6,7,8,9,9~{a}-octahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]cyclohexane-1,3-diol


Mass: 432.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C28H48O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: (NH4)2SO4 1.5M

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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: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.64→47.51 Å / Num. obs: 10563 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 32.4
Reflection shellResolution: 2.64→2.73 Å / Num. unique obs: 1024 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→47.5 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1057 10.02 %
Rwork0.2036 --
obs0.2095 10551 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 31 39 2071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.94
X-RAY DIFFRACTIONf_dihedral_angle_d17.319806
X-RAY DIFFRACTIONf_chiral_restr0.051317
X-RAY DIFFRACTIONf_plane_restr0.007355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.760.32031260.25771135X-RAY DIFFRACTION99
2.76-2.90.30531280.24251140X-RAY DIFFRACTION100
2.9-3.090.33271280.24971159X-RAY DIFFRACTION100
3.09-3.320.28591300.22821164X-RAY DIFFRACTION100
3.32-3.660.30161300.20751172X-RAY DIFFRACTION100
3.66-4.190.23151310.18351180X-RAY DIFFRACTION100
4.19-5.270.2411350.16741209X-RAY DIFFRACTION100
5.28-47.50.24591490.21441335X-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)
14.6803-1.2071-1.89926.72021.00367.9533-0.3193-0.3811-0.55220.3765-0.06180.21460.5293-0.13770.36260.4994-0.05280.0350.58120.06660.4896-27.899121.10720.1621
24.5165-1.9546-2.28945.14783.36035.3006-0.3589-0.9639-0.09671.09980.12890.09550.52470.56270.17590.786-0.0502-0.10790.83410.03380.5095-23.751827.97977.804
35.82170.07580.59495.96551.97345.71960.46350.54260.1950.2949-0.4253-0.88490.39140.8993-0.19820.6066-0.05710.03650.70640.06160.6334-18.546422.7032-16.8159
48.89022.3867-2.08948.7691.74232.04660.2995-0.41122.2195-0.39370.0433-0.2624-1.75780.9876-0.64390.9787-0.08980.04980.7347-0.08330.7694-24.091837.8911-14.7684
53.2696-2.1337-3.40776.77955.51827.50210.0663-0.10130.22130.2943-0.38730.68560.0321-0.44340.32160.4146-0.04460.00390.5216-0.02580.4709-33.67428.9468-4.7549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 284 through 376 )
2X-RAY DIFFRACTION2chain 'A' and (resid 377 through 432 )
3X-RAY DIFFRACTION3chain 'A' and (resid 433 through 452 )
4X-RAY DIFFRACTION4chain 'B' and (resid 687 through 695 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 283 )

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