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- PDB-7oxu: VDR complex - calcitroic acid -

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Basic information

Entry
Database: PDB / ID: 7oxu
TitleVDR complex - calcitroic acid
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / nuclear receptor / agonist
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition ...heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / vitamin D binding / calcitriol binding / lithocholic acid binding / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / lens development in camera-type eye / nuclear thyroid hormone receptor binding / embryonic hemopoiesis / positive regulation of intracellular estrogen receptor signaling pathway / hematopoietic stem cell proliferation / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / heart looping / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / general transcription initiation factor binding / negative regulation of neuron differentiation / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / calcium ion homeostasis / animal organ regeneration / ubiquitin ligase complex / intracellular steroid hormone receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / ossification / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / nuclear estrogen receptor binding / promoter-specific chromatin binding / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / brain development / Heme signaling / mRNA transcription by RNA polymerase II / cell morphogenesis / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / protein import into nucleus / transcription corepressor activity / nuclear receptor activity / ubiquitin protein ligase activity / Circadian Clock / angiogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell differentiation / transcription coactivator activity / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin binding / chromatin
Similarity search - Function
Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / 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 ...Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / 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
calcitroic acid / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsRochel, N. / Arnold, L.A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: To Be Published
Title: VDR complex - calcitroic acid
Authors: Arnold, L.A.
History
DepositionJun 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 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

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Assembly

Deposited unit
A: Vitamin D3 receptor A
B: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6183
Polymers35,2432
Non-polymers3751
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-11 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.728, 65.728, 264.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
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: 34030.688 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 Mediator of RNA polymerase II transcription subunit 1 / Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome ...Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TR-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


Mass: 1212.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-2QI / calcitroic acid / (3~{R})-3-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[(2~{Z})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]butanoic acid / Calcitroic acid


Mass: 374.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C23H34O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Mes pH 6 and 1.8 M lithium 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 EIGER X 9M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.39→29.43 Å / Num. obs: 14257 / % possible obs: 99.22 % / Redundancy: 20 % / Biso Wilson estimate: 71.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.26
Reflection shellResolution: 2.394→2.479 Å / Num. unique obs: 1361 / CC1/2: 0.433

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2.39→28.47 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1224 10 %
Rwork0.1934 11022 -
obs0.2001 12246 85.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.24 Å2 / Biso mean: 61.993 Å2 / Biso min: 28.92 Å2
Refinement stepCycle: final / Resolution: 2.39→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 27 48 2077
Biso mean--50.88 63.3 -
Num. residues----249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.490.3775700.355362869846
2.49-2.60.4046920.336783592760
2.6-2.740.39631320.33441172130485
2.74-2.910.37621490.26221336148597
2.91-3.130.34781530.24461377153098
3.13-3.450.28471520.20821377152997
3.45-3.950.24571520.15741368152096
3.95-4.970.17811570.13251417157496
4.97-29.430.23031670.18081512167995
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)
17.14035.04656.37538.32136.42559.1262-0.3848-0.40120.4359-0.3573-0.27220.1163-0.696-0.33380.65350.34880.0950.02840.46540.00110.28396.030945.123241.1847
22.08920.0548-0.04583.10811.14395.5053-0.0946-0.2832-0.01410.28220.0695-0.00630.2254-0.03230.01510.42110.0503-0.01890.46380.02660.24038.760634.516443.5743
32.1705-2.13421.80884.8448-4.68714.6041-0.0320.8210.0156-0.7051-0.3162-0.6535-0.14871.49880.22810.5691-0.0375-0.03280.764-0.04390.424321.487138.702429.625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 154 through 254 )A154 - 254
2X-RAY DIFFRACTION2chain 'A' and (resid 255 through 452 )A255 - 452
3X-RAY DIFFRACTION3chain 'B' and (resid 640 through 649 )B640 - 649

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