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- PDB-3afr: Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3... -

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Basic information

Entry
Database: PDB / ID: 3afr
TitleCrystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex
Components
  • 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION/Transcription regulator / Vitamin D Receptor / nuclear receptor / agonist / antagonist / vitamin D derivative / DNA-binding / Nucleus / Receptor / Transcription / Transcription regulation / TRANSCRIPTION-Transcription regulator complex
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / negative regulation of phosphate transmembrane transport / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / cell-cell junction maintenance / positive regulation of apoptotic process involved in mammary gland involution ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / negative regulation of phosphate transmembrane transport / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / cell-cell junction maintenance / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / cellular response to vitamin D / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / nuclear retinoic acid receptor binding / vitamin D binding / mediator complex / response to aldosterone / cellular response to thyroid hormone stimulus / phosphate ion transmembrane transport / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / negative regulation of ossification / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / intestinal absorption / regulation of calcium ion transport / mammary gland branching involved in pregnancy / nuclear steroid receptor activity / decidualization / negative regulation of keratinocyte proliferation / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / intracellular receptor signaling pathway / heterochromatin / lactation / T-tubule / animal organ morphogenesis / skeletal system development / transcription coregulator activity / apoptotic signaling pathway / euchromatin / response to calcium ion / caveola / mRNA transcription by RNA polymerase II / nuclear receptor activity / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / nuclear matrix / cell morphogenesis / intracellular calcium ion homeostasis / calcium ion transport / response to estradiol / heart development / sequence-specific DNA binding / cell differentiation / signaling receptor complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / nucleoplasm / nucleus / cytosol
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-ICJ / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D3 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Xenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsInaba, Y. / Nakabayashi, M. / Itoh, T. / Ikura, T. / Ito, N. / Yamamoto, K.
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2010
Title: 22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity
Authors: Inaba, Y. / Nakabayashi, M. / Itoh, T. / Yoshimoto, N. / Ikura, T. / Ito, N. / Shimizu, M. / Yamamoto, K.
History
DepositionMar 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6393
Polymers32,1662
Non-polymers4731
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.448, 43.394, 41.992
Angle α, β, γ (deg.)90.000, 95.341, 90.000
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 / Fragment: Ligand binding domain, residues 116-423 / Mutation: deletion mutant, residues 165-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: VDR, NR1I1 / Plasmid: PET-14B / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P13053
#2: Protein/peptide 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 / Mediator complex subunit 1 / peroxisome proliferator-activated receptor


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP205 NR2 BOX peptide, residues 624-636 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / Source: (synth.) Xenopus tropicalis (tropical clawed frog) / References: UniProt: A1L0Z0
#3: Chemical ChemComp-ICJ / (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethylhexyl]-7a-methyloctahydro-4H-inden-4-yli dene}ethylidene]-4-methylidenecyclohexane-1,3-diol / 22S-butyl-1a,24R-dihydroxyvitamin D3


Mass: 472.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H52O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.16 Å3/Da / Density % sol: 43.15 % / Mosaicity: 0.452 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 19085 / Num. obs: 18614 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Χ2: 2.502 / Net I/σ(I): 36.97
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.211 / Num. unique all: 1670 / Χ2: 1.678 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RK3

1rk3


Resolution: 2→41.74 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 137588 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1727 9.8 %RANDOM
Rwork0.216 ---
all-19085 --
obs-17660 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.389 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 78.75 Å2 / Biso mean: 41.247 Å2 / Biso min: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1--19.4 Å20 Å2-4.12 Å2
2--26.07 Å20 Å2
3----6.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 34 60 2109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 209 7.9 %
Rwork0.32 2426 -
all-2635 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2IC1_par.paramIC1_top.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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