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- PDB-4ynk: Crystal structure of vitamin D receptor ligand binding domain com... -

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Basic information

Entry
Database: PDB / ID: 4ynk
TitleCrystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound
Components
  • Coactivator peptide drip from cDNA FLJ50196, highly similar to Peroxisome proliferator-activated receptor-binding protein
  • Vitamin D3 receptor,Vitamin D3 receptor
KeywordsTRANSCRIPTION / Hormone receptor
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 / retinal pigment epithelium development / SUMOylation of intracellular receptors / 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 / retinal pigment epithelium development / SUMOylation of intracellular receptors / 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 retinoic acid receptor binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / phosphate ion transmembrane transport / ventricular trabecula myocardium morphogenesis / 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 / 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 / intestinal absorption / nuclear thyroid hormone receptor binding / negative regulation of ossification / 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 / 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 / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of keratinocyte proliferation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / animal organ regeneration / erythrocyte 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 / T-tubule / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / animal organ morphogenesis / nuclear receptor binding / skeletal system development / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / apoptotic signaling pathway / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / euchromatin / PPARA activates 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-YW2 / 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: 2.3 Å
AuthorsWatarai, Y. / Ikura, T. / Ito, N.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Synthesis, Biological Activities, and X-ray Crystal Structural Analysis of 25-Hydroxy-25(or 26)-adamantyl-17-[20(22),23-diynyl]-21-norvitamin D Compounds
Authors: Watarai, Y. / Ishizawa, M. / Ikura, T. / Zacconi, F.C. / Uno, S. / Ito, N. / Mourino, A. / Tokiwa, H. / Makishima, M. / Yamada, S.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / refine
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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,Vitamin D3 receptor
C: Coactivator peptide drip from cDNA FLJ50196, highly similar to Peroxisome proliferator-activated receptor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6673
Polymers32,1662
Non-polymers5011
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.437, 37.290, 41.121
Angle α, β, γ (deg.)90.00, 98.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin D3 receptor,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 116-164,212-423,UNP residues 116-164,212-423
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 Coactivator peptide drip from cDNA FLJ50196, highly similar to Peroxisome proliferator-activated receptor-binding protein


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648*PLUS
#3: Chemical ChemComp-YW2 / (1R,3R,7E,17beta)-17-{(5S)-5-hydroxy-5-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-1-yl]penta-1,3-diyn-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol


Mass: 500.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H44O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.85 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: MOPS, Sodium Formate, PEG4000, Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12259 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.08 / Rrim(I) all: 0.151 / Χ2: 2.216 / Net I/av σ(I): 15.479 / Net I/σ(I): 7.3 / Num. measured all: 42675
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.40.6795960.740.430.8061.52699.8
2.24-2.283.50.6495980.7640.4070.7681.64899.8
2.28-2.323.50.5546220.7690.3480.6561.69699.4
2.32-2.373.60.5335810.8330.330.6291.65899.7
2.37-2.423.50.5026250.8670.3110.5921.63299.7
2.42-2.483.50.4626000.8880.2890.5461.859100
2.48-2.543.60.4456100.8730.2740.5241.96799.7
2.54-2.613.50.3646060.8930.2270.431.89599.8
2.61-2.693.60.3266040.9160.2020.3852.02499.8
2.69-2.773.50.2886190.9410.1790.342.15799.8
2.77-2.873.50.2456030.9480.1540.292.22999.7
2.87-2.993.50.2386020.9430.150.2822.31599.8
2.99-3.123.50.1966360.960.1230.2322.613100
3.12-3.293.50.1675990.970.1060.1992.77499.8
3.29-3.493.40.1246210.9840.0790.1482.82599.5
3.49-3.763.40.0996170.9850.0640.1183.14699.7
3.76-4.143.40.0776160.990.0490.0922.92199.5
4.14-4.743.30.0626200.9950.0410.0752.92399.8
4.74-5.973.50.066330.9950.0370.0712.185100
5.97-503.40.0486510.9970.030.0572.499.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNS1.3refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZL9

2zl9


Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 1039 9.7 %Random
Rwork0.2015 8923 --
obs-9962 92.8 %-
Solvent computationBsol: 53.7986 Å2
Displacement parametersBiso max: 78.15 Å2 / Biso mean: 37.7062 Å2 / Biso min: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1--17.414 Å20 Å2-1.723 Å2
2--4.863 Å20 Å2
3---12.552 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 37 47 2093
Biso mean--28.9 38.25 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3731.5
X-RAY DIFFRACTIONc_scbond_it2.0912
X-RAY DIFFRACTIONc_mcangle_it2.2422
X-RAY DIFFRACTIONc_scangle_it3.0442.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6YW2b_param

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