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- PDB-6fo9: Vitamin D nuclear receptor complex 2 -

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Basic information

Entry
Database: PDB / ID: 6fo9
TitleVitamin D nuclear receptor complex 2
Components
  • Nuclear receptor coactivator 1
  • Vitamin D3 receptor A
KeywordsGENE REGULATION
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D 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 ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D 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 / Synthesis of bile acids and bile salts / estrous cycle / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / calcium ion homeostasis / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ossification / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / nuclear estrogen 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 / 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 / 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 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 / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-E0E / 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: 2.701 Å
AuthorsRochel, N.
Funding support France, Spain, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0024-01 France
Spanish Ministry of Economy and CompetitivenessSAF2015-69221-R Spain
CitationJournal: J. Med. Chem. / Year: 2018
Title: Aromatic-Based Design of Highly Active and Noncalcemic Vitamin D Receptor Agonists.
Authors: Gogoi, P. / Seoane, S. / Sigueiro, R. / Guiberteau, T. / Maestro, M.A. / Perez-Fernandez, R. / Rochel, N. / Mourino, A.
History
DepositionFeb 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 24, 2021Group: 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
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,1053
Polymers35,6932
Non-polymers4131
Water27015
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)72,2106
Polymers71,3854
Non-polymers8252
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3900 Å2
ΔGint-33 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.010, 66.010, 264.460
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: 33916.543 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9PTN2
#2: Protein/peptide Nuclear receptor coactivator 1


Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS
#3: Chemical ChemComp-E0E / (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]hex-2-enylidene]cyclohexane-1,3-diol


Mass: 412.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H40O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0721 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 16314 / % possible obs: 92.7 % / Redundancy: 5.4 % / Rsym value: 0.063 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.314 / % possible all: 72.6

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Processing

Software
NameVersionClassification
PHENIXdev_1796refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2.701→24.856 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.96
RfactorNum. reflection% reflection
Rfree0.2248 475 4.91 %
Rwork0.1972 --
obs0.1985 9671 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.701→24.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 30 15 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032066
X-RAY DIFFRACTIONf_angle_d0.7392785
X-RAY DIFFRACTIONf_dihedral_angle_d15.353799
X-RAY DIFFRACTIONf_chiral_restr0.026313
X-RAY DIFFRACTIONf_plane_restr0.004363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7007-3.09090.30931480.26242931X-RAY DIFFRACTION94
3.0909-3.89180.24861570.21953069X-RAY DIFFRACTION97
3.8918-24.85690.20181700.17883196X-RAY DIFFRACTION95
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)
13.3940.38791.36485.51023.44852.6857-0.1669-0.47141.1053-0.35930.0492-1.0652-0.76070.7425-0.14880.9980.2063-0.23311.3751-0.24760.948814.927152.604751.8766
23.8489-1.37791.32054.80323.46478.6061-0.2801-0.390.1906-0.2262-0.07060.4516-1.0552-0.89260.56850.95340.1322-0.19081.0009-0.08780.8724-2.41438.996430.2475
33.3266-0.62470.54924.03293.34656.8268-0.3596-0.69060.70430.08390.461-0.3459-0.22480.3179-0.2220.71050.0652-0.10690.8177-0.07210.708113.183238.82538.3637
43.4774-0.88550.36195.87823.51687.5243-0.0545-0.5991-0.14830.3027-0.42771.43570.2933-2.20620.73890.9601-0.03740.02481.5304-0.14670.9722-6.785134.026738.8178
54.1444-0.47720.46069.45865.5393.5585-0.1038-1.4753-0.96041.3756-0.02140.47841.1963-1.21870.44441.014-0.02760.05741.51120.01020.8837-1.04829.941348.8177
63.358-0.88710.01535.97263.04387.9324-0.1758-0.68350.08581.01660.3847-0.53290.75650.3347-0.35511.10470.2718-0.17721.2945-0.13310.76115.424340.89254.1603
72.3307-0.30720.69776.40524.36053.2551-0.3507-0.8444-0.3861.60560.46380.09151.58190.8438-0.23551.16090.087-0.05410.99850.0830.788.76227.704446.4214
83.52251.14212.01176.85363.13457.33980.17610.1429-0.71330.44450.0621-0.931.04270.4462-0.38230.8260.0469-0.09050.9777-0.08380.747214.25530.927627.785
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 254 )
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 334 )
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 351 )
6X-RAY DIFFRACTION6chain 'A' and (resid 352 through 404 )
7X-RAY DIFFRACTION7chain 'A' and (resid 405 through 431 )
8X-RAY DIFFRACTION8chain 'A' and (resid 432 through 652 )

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