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- PDB-8pz7: crystal structure of VDR complex with D-Bishomo-1a,25-dihydroxyvi... -

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Basic information

Entry
Database: PDB / ID: 8pz7
Titlecrystal structure of VDR complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 57
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 / calcitriol binding / vitamin D binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / locomotor rhythm ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / calcium ion homeostasis / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ossification / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / : / 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 / 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 / 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 / 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
Chem-IG0 / 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: 2.93 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 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._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)36,0873
Polymers35,6412
Non-polymers4471
Water43224
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)72,1746
Polymers71,2814
Non-polymers8932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4060 Å2
ΔGint-32 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 66.240, 264.040
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-IG0 / (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{R},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,8,9,9~{a}-hexahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-methyl-cyclohexane-1,3-diol


Mass: 446.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NH4Acetate 3.5M, BisTrisPropane 0.1M pH 7

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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: 2.93→48.07 Å / Num. obs: 8045 / % possible obs: 99.6 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 25.4
Reflection shellResolution: 2.93→3.04 Å / Num. unique obs: 750 / CC1/2: 0.948

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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: 2.93→48.06 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2571 802 10.03 %
Rwork0.1962 --
obs0.2023 7998 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 32 24 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.914
X-RAY DIFFRACTIONf_dihedral_angle_d17.72807
X-RAY DIFFRACTIONf_chiral_restr0.05315
X-RAY DIFFRACTIONf_plane_restr0.01354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.120.36491240.33281116X-RAY DIFFRACTION96
3.12-3.360.33971310.23621169X-RAY DIFFRACTION100
3.36-3.70.28081310.21471176X-RAY DIFFRACTION99
3.7-4.230.26411320.18591182X-RAY DIFFRACTION100
4.23-5.330.2271340.16611212X-RAY DIFFRACTION100
5.33-48.060.23461500.18721341X-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)
12.7507-0.5997-2.27736.725-5.80017.90240.31020.07891.64750.4103-0.06150.598-1.4529-0.4352-0.36990.7591-0.12870.16811.0158-0.18990.9277-39.487839.66096.3595
25.27322.40983.86458.05053.82593.4550.3796-0.40040.00120.0819-0.09961.3932-0.4917-1.6529-0.29250.65020.0267-0.0571.0904-0.14830.971-41.609723.3696-10.7686
32.96412.27913.53285.7909-1.30858.27290.1875-0.9726-0.5904-0.3787-0.03350.21521.3338-0.5185-0.29370.9673-0.12220.13830.8254-0.08740.7903-31.291411.2078-16.8035
45.4132-1.2114-1.98433.37210.11877.4870.1394-0.5531-0.02780.2338-0.19740.28690.0959-0.15970.07730.5528-0.08390.05450.6637-0.03760.4051-29.918527.7498-4.7352
52.51861.6542-1.98123.36041.13785.86340.0274-0.2033-0.95840.896-0.66080.57151.78-0.48420.67911.4101-0.20510.14710.7276-0.02551.124-32.837310.7331-8.4653
69.6904-2.6062-3.78823.00832.63356.8983-0.8207-0.9843-0.48670.7370.43710.13280.76970.14860.3360.9038-0.0155-0.06230.7683-0.00450.5829-31.155821.75075.9224
77.4047-2.0787-3.69762.66063.33587.7658-0.1688-1.29590.3450.69360.3298-0.20420.32821.2115-0.16770.7929-0.033-0.0290.974-0.06960.5722-24.372330.07357.3383
84.01020.60570.11116.01253.44566.2056-0.0189-0.1757-0.22680.19990.3904-0.73770.32420.8516-0.26620.68080.07930.10160.8191-0.04020.6527-19.116322.0786-16.9235
97.3373.2957-0.96574.95033.61364.84640.8046-0.25990.89990.0998-0.1138-0.0264-1.76911.1559-0.71431.0773-0.1007-0.0020.6952-0.07810.7481-23.605938.1852-15.3095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 155 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 315 )
5X-RAY DIFFRACTION5chain 'A' and (resid 316 through 334 )
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 366 )
7X-RAY DIFFRACTION7chain 'A' and (resid 367 through 431 )
8X-RAY DIFFRACTION8chain 'A' and (resid 432 through 451 )
9X-RAY DIFFRACTION9chain 'B' and (resid 686 through 695 )

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