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- PDB-5xpo: Crystal structure of VDR-LBD complexed with 25-(hydroxyphenyl)-2-... -

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Basic information

Entry
Database: PDB / ID: 5xpo
TitleCrystal structure of VDR-LBD complexed with 25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / vitamin D3 / VDR / VDRE / RXR / co-factors
Function / homology
Function and homology information


positive regulation of parathyroid hormone secretion / negative regulation of bone trabecula formation / mammary gland branching involved in pregnancy / Vitamin D (calciferol) metabolism / retinal pigment epithelium development / positive regulation of apoptotic process involved in mammary gland involution / androgen biosynthetic process / regulation of RNA biosynthetic process / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway ...positive regulation of parathyroid hormone secretion / negative regulation of bone trabecula formation / mammary gland branching involved in pregnancy / Vitamin D (calciferol) metabolism / retinal pigment epithelium development / positive regulation of apoptotic process involved in mammary gland involution / androgen biosynthetic process / regulation of RNA biosynthetic process / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / cellular response to vitamin D / lens development in camera-type eye / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / ventricular trabecula myocardium morphogenesis / negative regulation of ossification / megakaryocyte development / negative regulation of keratinocyte proliferation / vitamin D binding / Generic Transcription Pathway / mediator complex / nuclear retinoic acid receptor binding / intestinal absorption / response to aldosterone / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / phosphate ion transmembrane transport / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / negative regulation of neuron differentiation / nuclear thyroid hormone receptor binding / cellular response to steroid hormone stimulus / histone acetyltransferase binding / LBD domain binding / decidualization / RSV-host interactions / regulation of calcium ion transport / nuclear receptor-mediated steroid hormone signaling pathway / keratinocyte differentiation / positive regulation of transcription initiation by RNA polymerase II / general transcription initiation factor binding / fat cell differentiation / nuclear retinoid X receptor binding / ubiquitin ligase complex / retinoic acid receptor signaling pathway / erythrocyte development / lactation / RNA polymerase II preinitiation complex assembly / intracellular receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / skeletal system development / heterochromatin / positive regulation of erythrocyte differentiation / BMAL1:CLOCK,NPAS2 activates circadian expression / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / animal organ morphogenesis / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / T-tubule / cellular response to epidermal growth factor stimulus / apoptotic signaling pathway / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator activity / Heme signaling / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / promoter-specific chromatin binding / cell morphogenesis / euchromatin / response to calcium ion / Transcriptional regulation of white adipocyte differentiation / chromatin DNA binding / Nuclear Receptor transcription pathway / protein-DNA complex / RNA polymerase II transcription regulator complex / caveola / intracellular calcium ion homeostasis / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coactivator binding / cellular response to amyloid-beta / nuclear matrix / calcium ion transport / heart development / transcription corepressor activity / response to estradiol / ubiquitin protein ligase activity / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / angiogenesis / Estrogen-dependent 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-8BL / 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: 2.28 Å
AuthorsKato, A. / Itoh, T. / Yamamoto, K.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying ...Title: Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
Authors: Kato, A. / Yamao, M. / Hashihara, Y. / Ishida, H. / Itoh, T. / Yamamoto, K.
History
DepositionJun 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
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 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)32,6453
Polymers32,1662
Non-polymers4791
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: We have reported cell based assay for the assembly of VDR and co-activator. Bioconjug. Chem. 2016, 27, 1750-1761.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.560, 43.390, 42.130
Angle α, β, γ (deg.)90.00, 95.48, 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: UNP residues 116-423 / Mutation: deletion mutant(residues 165-211)
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 / 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 / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: UNP residues 640-652
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
Production host: synthetic construct (others) / References: UniProt: Q15648
#3: Chemical ChemComp-8BL / (5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one / 25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3


Mass: 478.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H42O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→41.74 Å / Num. obs: 11584 / % possible obs: 95.9 % / Redundancy: 1.9 % / Net I/σ(I): 7.7

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→41.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.263 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.274 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27478 591 4.9 %RANDOM
Rwork0.21265 ---
obs0.21572 11584 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.061 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å20 Å2-0.49 Å2
2--3.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.28→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 35 61 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192052
X-RAY DIFFRACTIONr_bond_other_d0.0010.022002
X-RAY DIFFRACTIONr_angle_refined_deg1.5832.0022780
X-RAY DIFFRACTIONr_angle_other_deg0.83234621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9355246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83424.36887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2581511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212243
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02442
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_it2.6293.539993
X-RAY DIFFRACTIONr_mcbond_other2.6273.537992
X-RAY DIFFRACTIONr_mcangle_it3.9355.2831236
X-RAY DIFFRACTIONr_mcangle_other3.9345.2851237
X-RAY DIFFRACTIONr_scbond_it2.7763.7211059
X-RAY DIFFRACTIONr_scbond_other2.7763.7211059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3285.4761545
X-RAY DIFFRACTIONr_long_range_B_refined6.127.9112397
X-RAY DIFFRACTIONr_long_range_B_other6.09927.9092398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 46 -
Rwork0.275 867 -
obs--96.72 %

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