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- PDB-1rk3: crystal structure of the rat vitamin D receptor ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 1rk3
Titlecrystal structure of the rat vitamin D receptor ligand binding domain complexed with 1,25-dihydroxyvitamin D3 and a synthetic peptide containing the NR2 box of DRIP 205
Components
  • Peroxisome proliferator-activated receptor binding protein
  • Vitamin D3 receptor
Keywordshormone/growth factor receptor / nuclear receptor-ligand complex / nuclear receptor-coactivator interactions / 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 / 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-VDX / 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: 2.2 Å
AuthorsVanhooke, J.L. / M Benning, M. / Bauer, C.B. / Pike, J.W. / DeLuca, H.F.
CitationJournal: Biochemistry / Year: 2004
Title: Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D(3) 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
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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

Downloads & links

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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)34,9713
Polymers34,5552
Non-polymers4171
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-8 kcal/mol
Surface area11750 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)69,9436
Polymers69,1094
Non-polymers8332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5810 Å2
ΔGint-35 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.726, 44.154, 42.072
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains one biological unit. The biological unit is composed of one molecule of VDR, one ligand molecule, and one molecule of the synthetic peptide

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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: Chain A, DEL(165-211)
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) CodonPlus 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 / TRIP2 / 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 / References: UniProt: Q15648
#3: Chemical ChemComp-VDX / 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL / 1,25 DIHYDROXY VITAMIN D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM R / Detector: CCD / Date: Oct 24, 2002
RadiationMonochromator: Montel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→42.44 Å / Num. all: 14565 / Num. obs: 14475 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rsym value: 0.052 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.198 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SAINTdata reduction
LSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1RJK

1rjk


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.508 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24255 727 5 %RANDOM
Rwork0.19048 ---
all0.19303 14468 --
obs0.19303 14468 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å2-0.62 Å2
2--3.31 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 30 92 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212061
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.992791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115247
X-RAY DIFFRACTIONr_chiral_restr0.0890.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021507
X-RAY DIFFRACTIONr_nbd_refined0.2080.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.21
X-RAY DIFFRACTIONr_mcbond_it0.8221.51253
X-RAY DIFFRACTIONr_mcangle_it1.56522032
X-RAY DIFFRACTIONr_scbond_it2.4383808
X-RAY DIFFRACTIONr_scangle_it3.9984.5759
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.271 41
Rwork0.199 936
obs-977

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