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- PDB-3wt7: Crystal structure of VDR-LBD complexed with 22R-Butyl-2-methylide... -

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Basic information

Entry
Database: PDB / ID: 3wt7
TitleCrystal structure of VDR-LBD complexed with 22R-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1 ,25-dihydroxyvitamin D3
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / Vitamin D3 / VDRE / RXR / co-factors / nuclear
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors / G0 to G1 transition / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / core mediator complex / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D binding / lithocholic acid binding / bile acid nuclear receptor activity / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of ossification / vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / positive regulation of vitamin D receptor signaling pathway / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / response to aldosterone / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / 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 keratinocyte proliferation / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / T-tubule / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / lactation / Regulation of lipid metabolism by PPARalpha / positive regulation of erythrocyte differentiation / liver development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / apoptotic signaling pathway / skeletal system development / nuclear receptor binding / nuclear estrogen receptor binding / promoter-specific chromatin binding / animal organ morphogenesis / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / brain development / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / euchromatin / caveola / 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 / 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-YA2 / 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: 2.4 Å
AuthorsAnami, Y. / Itoh, T. / Yamamoto, K.
CitationJournal: J.Med.Chem. / Year: 2014
Title: A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
Authors: Anami, Y. / Itoh, T. / Egawa, D. / Yoshimoto, N. / Yamamoto, K.
History
DepositionApr 8, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / 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)32,6533
Polymers32,1662
Non-polymers4871
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.210, 44.310, 45.810
Angle α, β, γ (deg.)90.00, 93.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-640-

HOH

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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 116-164, 212-423
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-YA2 / (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol


Mass: 486.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H54O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.07 %
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: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2013
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→63.98 Å / Num. obs: 8562 / % possible obs: 84.3 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
SERGUIdata collection
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 2.4→45.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.463 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 408 4.8 %RANDOM
Rwork0.17623 ---
obs0.17709 8153 83.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.108 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-1.28 Å2
2--1.77 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 35 47 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192083
X-RAY DIFFRACTIONr_bond_other_d00.022047
X-RAY DIFFRACTIONr_angle_refined_deg1.68722820
X-RAY DIFFRACTIONr_angle_other_deg3.48334731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7915248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04524.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74115380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212267
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02445
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 30 -
Rwork0.209 605 -
obs--83.66 %
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)
10.4244-0.13820.06520.2616-0.15820.10780.0212-0.00620.0170.0077-0.0207-0.0062-0.0144-0.0144-0.00050.0563-0.00320.0110.0847-0.00330.025814.92760.977357.134
215.33036.936-1.19558.0256-2.4541.51470.34580.2108-0.5412-0.218-0.2161-0.00220.16340.1449-0.12960.05090.0567-0.03640.0814-0.02860.03999.674-10.070642.2817
31.37750.25833.9860.04890.747211.53480.1542-0.0973-0.02170.0293-0.0559-0.01150.5533-0.2793-0.09830.15290.02310.0740.03430.01970.16016.03494.186258.2741
40.3868-0.0531-0.00950.0246-0.0390.1752-0.01770.0107-0.06320.0283-0.00530.01730.01080.00670.0230.1005-0.00430.05240.05560.00780.038515.5271-0.458955.0187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 420
2X-RAY DIFFRACTION2C625 - 635
3X-RAY DIFFRACTION3A501
4X-RAY DIFFRACTION4A601 - 647

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