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- PDB-3wtq: Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylide... -

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Basic information

Entry
Database: PDB / ID: 3wtq
TitleCrystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / Vitamin D3 / VDRE / RXR / co-factors
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / core mediator complex / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / cellular response to vitamin D / vitamin D binding / calcitriol binding / lithocholic acid binding / nuclear retinoic acid receptor binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / phosphate ion transmembrane transport / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / positive regulation of hepatocyte proliferation / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / intestinal absorption / nuclear thyroid hormone receptor binding / negative regulation of ossification / lens development in camera-type eye / embryonic hemopoiesis / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / response to aldosterone / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / regulation of calcium ion transport / decidualization / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of keratinocyte proliferation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / animal organ regeneration / erythrocyte development / nuclear retinoid X receptor binding / heterochromatin / retinoic acid receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / intracellular receptor signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / T-tubule / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / animal organ morphogenesis / nuclear receptor binding / skeletal system development / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / apoptotic signaling pathway / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / euchromatin / PPARA activates gene expression
Similarity search - Function
: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-YS9 / Vitamin D3 receptor / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakabayashi, M. / Inaba, Y. / Itoh, T. / Anami, Y. / Ikura, T. / Ito, N. / Yamamoto, K.
CitationJournal: To be Published
Title: Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
Authors: Nakabayashi, M. / Inaba, Y. / Itoh, T. / Anami, Y. / Ikura, T. / Ito, N. / Yamamoto, K.
History
DepositionApr 15, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6393
Polymers32,1662
Non-polymers4731
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.286, 43.851, 42.321
Angle α, β, γ (deg.)90.00, 96.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin D3 receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor / Nuclear receptor subfamily 1 group I member 1


Mass: 30595.037 Da / Num. of mol.: 1 / Fragment: Ligand binding domain, UNP residues 116-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP205 NR2 BOX peptide, UNP residues 640-652 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-YS9 / (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol


Mass: 472.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H52O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16456 / % possible obs: 99.3 %

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Processing

Software
NameVersionClassification
SERGUIdata collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.61 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.493 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 827 5.1 %RANDOM
Rwork0.2319 ---
obs0.23408 15502 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.341 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å2-1 Å2
2--5.57 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 34 22 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192187
X-RAY DIFFRACTIONr_bond_other_d00.022136
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9992967
X-RAY DIFFRACTIONr_angle_other_deg3.58234936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0045263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5324.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99815388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.761511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212388
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02469
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 66 -
Rwork0.337 1121 -
obs--100 %
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)
11.2523-0.2359-0.14370.0685-0.00840.20560.1331-0.0065-0.0606-0.0039-0.04350.0095-0.09670.0169-0.08960.2146-0.0182-0.00330.1034-0.01340.180718.8128-1.183219.501
28.0313.4679-4.73312.2458-3.34095.0489-0.19410.2439-0.4693-0.1867-0.2035-0.24380.30430.35420.39760.0781-0.00040.0640.2609-0.16140.24396.3612-12.721511.2188
30.6201-0.17150.06410.0745-0.12270.45850.09870.03820.0096-0.0057-0.0211-0.005-0.05090.0108-0.07760.2212-0.01250.01490.0595-0.01380.241215.07910.707817.5005
40.4904-0.08910.96873.93741.32552.49970.26530.07040.2561-0.0119-0.6439-0.3730.5198-0.06610.37860.1881-0.03810.13760.22830.08710.160912.73481.973825.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 420
2X-RAY DIFFRACTION2C625 - 635
3X-RAY DIFFRACTION3A601 - 622
4X-RAY DIFFRACTION4A501

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