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- PDB-3vt9: Crystal structures of rat VDR-LBD with W282R mutation -

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Basic information

Entry
Database: PDB / ID: 3vt9
TitleCrystal structures of rat VDR-LBD with W282R mutation
Components
  • COACTIVATOR PEPTIDE DRIP
  • Vitamin D3 receptor
KeywordsHORMONE RECEPTOR / Transcription
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D binding / lithocholic acid binding / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / response to aldosterone / mammary gland branching involved in pregnancy / regulation of calcium ion transport / decidualization / negative regulation of keratinocyte proliferation / heterochromatin / nuclear retinoid X receptor binding / T-tubule / lactation / skeletal system development / apoptotic signaling pathway / animal organ morphogenesis / mRNA transcription by RNA polymerase II / cell morphogenesis / euchromatin / caveola / nuclear matrix / response to calcium ion / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to amyloid-beta / calcium ion transport / response to estradiol / heart development / sequence-specific DNA binding / cell differentiation / receptor complex / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / 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 / DNA binding / zinc ion binding / nucleus
Similarity search - Function
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. ...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-YI4 / Vitamin D3 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsNakabayashi, M. / Shimizu, M. / Ikura, T. / Ito, N.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
Authors: Nakabayashi, M. / Tsukahara, Y. / Iwasaki-Miyamoto, Y. / Mihori-Shimazaki, M. / Yamada, S. / Inaba, S. / Oda, M. / Shimizu, M. / Makishima, M. / Tokiwa, H. / Ikura, T. / Ito, N.
History
DepositionMay 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: COACTIVATOR PEPTIDE DRIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6243
Polymers32,1372
Non-polymers4871
Water70339
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-10 kcal/mol
Surface area12150 Å2
MethodPISA
2
A: Vitamin D3 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0532
Polymers30,5661
Non-polymers4871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.714, 42.050, 41.972
Angle α, β, γ (deg.)90.00, 95.63, 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: 30566.021 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 116-423 / Mutation: W282R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nr1i1, Vdr / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P13053
#2: Protein/peptide COACTIVATOR PEPTIDE DRIP


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIS
#3: Chemical ChemComp-YI4 / (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS-Na, sodium formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorDate: Feb 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 10561 / Biso Wilson estimate: 24.8 Å2
Reflection shellResolution: 2.35→2.43 Å

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 2.35→35.29 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 116145.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1087 10.3 %RANDOM
Rwork0.198 ---
obs0.198 10561 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1422 Å2 / ksol: 0.348529 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--12.75 Å20 Å2-3.64 Å2
2--12.07 Å20 Å2
3---0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.35→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 35 39 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it4.854
X-RAY DIFFRACTIONc_scangle_it6.15
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 153 9.7 %
Rwork0.234 1419 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3YI4_3.paramYI4_3.top

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