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- PDB-3w0j: Crystal Structure of Rat VDR Ligand Binding Domain in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 3w0j
TitleCrystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 Receptor
KeywordsTRANSCRIPTION / GENE REGULATION
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 / SUMOylation of intracellular receptors / retinal pigment epithelium development / 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 / SUMOylation of intracellular receptors / retinal pigment epithelium development / 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 receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / nuclear retinoic acid receptor binding / phosphate ion transmembrane transport / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / response to aldosterone / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / intestinal absorption / 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 / negative regulation of ossification / nuclear thyroid hormone receptor binding / 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 / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / RSV-host interactions / erythrocyte development / fat cell differentiation / mammary gland branching involved in pregnancy / regulation of calcium ion transport / nuclear steroid receptor activity / monocyte differentiation / decidualization / general transcription initiation factor binding / animal organ regeneration / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / ubiquitin ligase complex / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / nuclear receptor-mediated steroid hormone signaling pathway / 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 / peroxisome proliferator activated receptor signaling pathway / T-tubule / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / cellular response to epidermal growth factor stimulus / positive regulation of erythrocyte differentiation / liver development / animal organ morphogenesis / nuclear estrogen receptor binding / nuclear receptor binding / skeletal system development / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / apoptotic signaling pathway / mRNA transcription by RNA polymerase II / promoter-specific chromatin binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / euchromatin
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-T08 / 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: 1.84 Å
AuthorsShimizu, T. / Asano, L. / Kuwabara, N. / Ito, I. / Waku, T. / Yanagisawa, J. / Miyachi, H.
CitationJournal: Febs Lett. / Year: 2013
Title: Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands.
Authors: Asano, L. / Ito, I. / Kuwabara, N. / Waku, T. / Yanagisawa, J. / Miyachi, H. / Shimizu, T.
History
DepositionOct 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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 / 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)30,7573
Polymers30,3262
Non-polymers4311
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-10 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.214, 42.390, 42.144
Angle α, β, γ (deg.)90.00, 94.89, 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: 28755.025 Da / Num. of mol.: 1
Fragment: LIGAND BINDING DOMAIN, UNP residues 121-164, 212-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nr1i1, Vdr / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor-interacting protein complex component DRIP205


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP 205 NR2 BOX PEPTIDE, UNP residues 640-652 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-T08 / (2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propan-2-yl]-2-methylphenoxy}propane-1,2-diol


Mass: 430.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H38O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MOPS (pH7.0), 16-18% PEG 4000, 0.2M sodium formate, 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 21, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40.86 Å / Num. all: 17613 / Num. obs: 17224 / % possible obs: 97.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 97.79

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RK3

1rk3


Resolution: 1.84→40.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.221 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.231 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25863 942 5.2 %RANDOM
Rwork0.22325 ---
all0.22508 17613 --
obs0.22508 17224 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.191 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.84→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 31 113 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9952848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9045252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58724.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4471512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211562
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7391.51276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36622076
X-RAY DIFFRACTIONr_scbond_it1.8313824
X-RAY DIFFRACTIONr_scangle_it2.8794.5772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 69 -
Rwork0.274 1248 -
obs--98.21 %

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