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- PDB-5b5b: Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-d... -

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Basic information

Entry
Database: PDB / ID: 5b5b
TitleCrystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / vitamin D3 / VDR / VDRE / RXR / co-factors / antagonist
Function / homology
Function and homology information


enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / dense fibrillar component / SUMOylation of intracellular receptors / thyroid hormone mediated signaling pathway / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / core mediator complex / regulation of vitamin D receptor signaling pathway / 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 / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / negative regulation of ossification / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / embryonic hemopoiesis / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / response to aldosterone / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / 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 neuron differentiation / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / animal organ regeneration / heterochromatin / ubiquitin ligase complex / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / 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 / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / skeletal system development / nuclear estrogen receptor binding / promoter-specific chromatin binding / apoptotic signaling pathway / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / animal organ morphogenesis / brain development / euchromatin / Heme signaling / mRNA transcription by RNA polymerase II / cell morphogenesis / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / intracellular calcium ion homeostasis
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. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...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-AKX / 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 / Resolution: 2 Å
AuthorsKato, A. / Itoh, T. / Yamamoto, K.
CitationJournal: Bioconjug.Chem. / Year: 2016
Title: Helix12-Stabilization Antagonist of Vitamin D Receptor
Authors: Kato, A. / Itoh, T. / Anami, Y. / Egawa, D. / Yamamoto, K.
History
DepositionMay 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Vitamin D3 receptor
F: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4706
Polymers64,3324
Non-polymers1,1382
Water5,513306
1
A: Vitamin D3 receptor
C: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7353
Polymers32,1662
Non-polymers5691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-10 kcal/mol
Surface area12660 Å2
MethodPISA
2
D: Vitamin D3 receptor
F: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7353
Polymers32,1662
Non-polymers5691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.060, 41.490, 83.890
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-736-

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.: 2 / Fragment: UNP RESIDUES 116-164, 212-423 / Mutation: 165-211 deletion
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.: 2 / Fragment: UNP residues 640-652 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-AKX / (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-oxidanyl-7-phenyl-6-(phenylmethyl)heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol / 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxy vitamin D3


Mass: 568.828 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H52O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30.14 Å / Num. obs: 30998 / % possible obs: 85.9 % / Redundancy: 2.8 % / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2→30.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.882 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22991 1529 4.9 %RANDOM
Rwork0.17999 ---
obs0.18251 29468 85.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.549 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0 Å2-0.55 Å2
2--1.61 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 84 306 4470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194256
X-RAY DIFFRACTIONr_bond_other_d0.0020.024154
X-RAY DIFFRACTIONr_angle_refined_deg1.6472.0055764
X-RAY DIFFRACTIONr_angle_other_deg0.86139594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1735505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70524.516186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79315768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3971523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214646
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02929
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_it2.0892.2342038
X-RAY DIFFRACTIONr_mcbond_other2.0892.2332037
X-RAY DIFFRACTIONr_mcangle_it3.2883.3212537
X-RAY DIFFRACTIONr_mcangle_other3.2883.3232538
X-RAY DIFFRACTIONr_scbond_it2.6462.5462218
X-RAY DIFFRACTIONr_scbond_other2.6452.5482219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2173.693228
X-RAY DIFFRACTIONr_long_range_B_refined6.42618.3775085
X-RAY DIFFRACTIONr_long_range_B_other6.39618.14985
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
Rfree0.294 91 -
Rwork0.228 1942 -
obs--76.95 %

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