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- PDB-5zwi: Interaction between Vitamin D receptor (VDR) and a ligand having ... -

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Basic information

Entry
Database: PDB / ID: 5zwi
TitleInteraction between Vitamin D receptor (VDR) and a ligand having a dienone group
Components
  • 13-meric peptide from DRIP205 NR2 BOX peptide
  • Vitamin D3 receptor
KeywordsHORMONE / HORMONE covalent modifier transcription factor VitaminD3 enone Michael addition electrophile
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 / ventricular trabecula myocardium morphogenesis / phosphate ion transmembrane transport / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / 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 / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / response to aldosterone / 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 / negative regulation of keratinocyte proliferation / hematopoietic stem cell differentiation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / 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 / apoptotic signaling pathway / positive regulation of transcription elongation by RNA polymerase II / 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-9KX / 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: 2.4 Å
AuthorsYoshizawa, M. / Itoh, T. / Anami, Y. / Kato, A. / Yoshimoto, N. / Yamamoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: J. Med. Chem. / Year: 2018
Title: Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
Authors: Yoshizawa, M. / Itoh, T. / Hori, T. / Kato, A. / Anami, Y. / Yoshimoto, N. / Yamamoto, K.
History
DepositionMay 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 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: 13-meric peptide from DRIP205 NR2 BOX peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5773
Polymers32,1662
Non-polymers4111
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.670, 42.400, 41.850
Angle α, β, γ (deg.)90.00, 95.96, 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 / 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 13-meric peptide from DRIP205 NR2 BOX peptide


Mass: 1570.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: Q15648*PLUS
#3: Chemical ChemComp-9KX / (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one


Mass: 410.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: 2.4→41.62 Å / Num. obs: 9413 / % possible obs: 88.7 % / Redundancy: 3.4 % / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementResolution: 2.4→41.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.983 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.995 / ESU R Free: 0.28 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22751 465 4.9 %RANDOM
Rwork0.20491 ---
obs0.20602 8948 87.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.017 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å2-0 Å2-0.94 Å2
2--5.39 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.4→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 30 67 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192069
X-RAY DIFFRACTIONr_bond_other_d0.0060.022020
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9962800
X-RAY DIFFRACTIONr_angle_other_deg1.09734667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7125248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27624.83189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46615376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.147159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212266
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02448
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_it1.8243.71001
X-RAY DIFFRACTIONr_mcbond_other1.8213.6981000
X-RAY DIFFRACTIONr_mcangle_it2.8525.5291246
X-RAY DIFFRACTIONr_mcangle_other2.855.5311247
X-RAY DIFFRACTIONr_scbond_it2.1853.9481068
X-RAY DIFFRACTIONr_scbond_other2.1843.9471069
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4415.8271555
X-RAY DIFFRACTIONr_long_range_B_refined5.52334.6888923
X-RAY DIFFRACTIONr_long_range_B_other5.51534.6838900
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
Rfree0.366 43 -
Rwork0.243 668 -
obs--88.88 %

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