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- PDB-5xpl: Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyp... -

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Basic information

Entry
Database: PDB / ID: 5xpl
TitleCrystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / vitamin D3 / VDR / VDRE / RXR / co-factors / SRC2-3 / antagonist
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / dense fibrillar component / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / dense fibrillar component / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / vitamin D binding / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / response to aldosterone / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / mammary gland branching involved in pregnancy / regulation of calcium ion transport / aryl hydrocarbon receptor binding / decidualization / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / negative regulation of keratinocyte proliferation / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / heterochromatin / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / T-tubule / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / skeletal system development / apoptotic signaling pathway / nuclear receptor binding / animal organ morphogenesis / circadian regulation of gene expression / euchromatin / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / cell morphogenesis / Transcriptional activation of mitochondrial biogenesis / intracellular calcium ion homeostasis / PPARA activates gene expression / Cytoprotection by HMOX1 / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / response to calcium ion / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / nuclear receptor activity / calcium ion transport / Circadian Clock / response to estradiol / heart development / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / receptor complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding
Similarity search - Function
Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 ...Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-8C9 / Vitamin D3 receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7243
Polymers32,1892
Non-polymers5351
Water1,63991
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 area1070 Å2
ΔGint-4 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.780, 44.910, 45.520
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-661-

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: 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 Nuclear receptor coactivator 2 / / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1593.844 Da / Num. of mol.: 1 / Fragment: UNP residues 740-752
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, BHLHE75, SRC2, TIF2 / Production host: synthetic construct (others) / References: UniProt: Q15596
#3: Chemical ChemComp-8C9 / (4~{S})-4-[(1~{R})-1-[(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 )cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one / 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3


Mass: 534.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H50O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MOPS-Na, Na-Formate, PEG 4000, Ethylenglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→64.26 Å / Num. obs: 14660 / % possible obs: 88.7 % / Redundancy: 2.9 % / Net I/σ(I): 11.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→64.26 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.31 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24173 748 5.1 %RANDOM
Rwork0.18607 ---
obs0.18883 13899 88.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å2-0.04 Å2
2--0.79 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.05→64.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 39 91 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192104
X-RAY DIFFRACTIONr_bond_other_d0.0020.022054
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9992850
X-RAY DIFFRACTIONr_angle_other_deg0.88934748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1735251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43324.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92115381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8991512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212305
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02459
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_it2.4012.3871007
X-RAY DIFFRACTIONr_mcbond_other2.3942.3841006
X-RAY DIFFRACTIONr_mcangle_it3.6463.5431257
X-RAY DIFFRACTIONr_mcangle_other3.6453.5461258
X-RAY DIFFRACTIONr_scbond_it3.1382.791097
X-RAY DIFFRACTIONr_scbond_other3.1362.7891098
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7734.0321594
X-RAY DIFFRACTIONr_long_range_B_refined6.37819.4832382
X-RAY DIFFRACTIONr_long_range_B_other6.36919.3182359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 39 -
Rwork0.158 737 -
obs--65.54 %

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