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- PDB-2o4j: Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain... -

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Basic information

Entry
Database: PDB / ID: 2o4j
TitleCrystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205
Components
  • Peroxisome proliferator-activated receptor-binding protein
  • Vitamin D3 receptor
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / Nuclear receptor-ligand complex / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
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-VD4 / Vitamin D3 receptor / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsVanhooke, J.L. / Benning, M.M. / DeLuca, H.F.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2007
Title: New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations.
Authors: Vanhooke, J.L. / Tadi, B.P. / Benning, M.M. / Plum, L.A. / Deluca, H.F.
#1: Journal: Biochemistry / Year: 2004
Title: Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D3 Hormone Analogues and a LXXLL-Containing Coactivator Peptide
Authors: Vanhooke, J.L. / Benning, M.M. / Bauer, C.B. / Pike, J.W. / DeLuca, H.F.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: Peroxisome proliferator-activated receptor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9693
Polymers34,5552
Non-polymers4151
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area11790 Å2
MethodPISA
2
A: Vitamin D3 receptor
C: Peroxisome proliferator-activated receptor-binding protein
hetero molecules

A: Vitamin D3 receptor
C: Peroxisome proliferator-activated receptor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9386
Polymers69,1094
Non-polymers8292
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5800 Å2
ΔGint-39 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.500, 42.400, 41.900
Angle α, β, γ (deg.)90.000, 96.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

DetailsThe biological unit is composed of one molecule of VDR (chain A), one molecule of the synthetic peptide (chain C), and one ligand molecule (residue name VD4). The asymmetric unit contains one biological unit.

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Components

#1: Protein Vitamin D3 receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor


Mass: 32983.730 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Mutation: residues Ser165 through Pro211 are deleted from the protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Plasmid: pET-29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) Codon Plus RIL / References: UniProt: P13053
#2: Protein/peptide Peroxisome proliferator-activated receptor-binding protein / PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component ...PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TRIP-2 / p53 regulatory protein RB18A / Vitamin D receptor-interacting protein complex component DRIP205 / Activator- recruited cofactor 205 kDa component / ARC205


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP 205 NR2 Box Peptide / Source method: obtained synthetically / Details: synthesized at UW-Madison Biotechnology Center / References: UniProt: Q15648
#3: Chemical ChemComp-VD4 / (1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol


Mass: 414.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 295 K / Method: macroseeding in batch / pH: 7
Details: PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM R / Detector: CCD / Date: Nov 30, 2005 / Details: Montel Optics
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→42.5 Å / Num. all: 27636 / Num. obs: 27577 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rsym value: 0.0448 / Net I/σ(I): 19.4
Reflection shellResolution: 1.74→1.85 Å / Redundancy: 3.54 % / Mean I/σ(I) obs: 2.86 / Num. unique all: 4160 / Rsym value: 0.321 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
SAINTdata reduction
LSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1RJK

1rjk


Resolution: 1.74→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.362 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1388 5 %RANDOM
Rwork0.199 ---
obs0.201 26241 98.43 %-
all-26241 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.413 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å2-0.43 Å2
2--2.91 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 30 212 2242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222073
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9952808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0275249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04524.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2531510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021530
X-RAY DIFFRACTIONr_nbd_refined0.2130.21034
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.29
X-RAY DIFFRACTIONr_mcbond_it1.0221.51312
X-RAY DIFFRACTIONr_mcangle_it1.62822043
X-RAY DIFFRACTIONr_scbond_it2.5073859
X-RAY DIFFRACTIONr_scangle_it3.8664.5765
LS refinement shellResolution: 1.74→1.786 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 74 -
Rwork0.302 1581 -
obs-1655 80.65 %

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