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- PDB-3a2h: Crystal structure of the rat vitamin D receptor ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 3a2h
TitleCrystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205
Components
  • Mediator of RNA polymerase II transcription subunit 1 peptide
  • Vitamin D3 receptor
KeywordsHORMONE RECEPTOR / TRANSCRIPTION / hormone/growth factor receptor / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc-finger / Activator / Receptor
Function / homology
Function and homology information


enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / dense fibrillar component / SUMOylation of intracellular receptors / thyroid hormone mediated signaling pathway / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / core mediator complex / regulation of vitamin D receptor signaling pathway / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / vitamin D binding / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / negative regulation of ossification / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / embryonic hemopoiesis / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / response to aldosterone / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / 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 / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / animal organ regeneration / heterochromatin / ubiquitin ligase complex / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / T-tubule / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / skeletal system development / nuclear estrogen receptor binding / promoter-specific chromatin binding / apoptotic signaling pathway / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / animal organ morphogenesis / brain development / euchromatin / Heme signaling / mRNA transcription by RNA polymerase II / cell morphogenesis / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / intracellular calcium ion homeostasis
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. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...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 / 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-TEJ / 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: 2.5 Å
AuthorsKakuda, S. / Takimoto-Kamimura, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone
Authors: Kakuda, S. / Ishizuka, S. / Eguchi, H. / Mizwicki, M.T. / Norman, A.W. / Takimoto-Kamimura, M.
History
DepositionMay 20, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 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
B: Mediator of RNA polymerase II transcription subunit 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0533
Polymers31,6262
Non-polymers4271
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-9 kcal/mol
Surface area11880 Å2
MethodPISA
2
A: Vitamin D3 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4822
Polymers30,0551
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Mediator of RNA polymerase II transcription subunit 1 peptide


  • defined by author
  • 1.57 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,5711
Polymers1,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.809, 45.349, 46.662
Angle α, β, γ (deg.)90.00, 100.13, 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: 30055.498 Da / Num. of mol.: 1 / Fragment: ligand binding domain, residues 116-423 / Mutation: DEL(165-211) mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1 peptide / DRIP 205 NR2 box peptide / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor- ...DRIP 205 NR2 box peptide / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / Vitamin D receptor-interacting protein complex component DRIP205 / Activator-recruited cofactor 205 kDa component


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-TEJ / (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one / (23S)-25-dehydro-1alpha-hydroxyvitamin D3-26,23-lactone


Mass: 426.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND TEJ CAN BE CALLED AS TEI-9647.
Sequence detailsTHIS PROTEIN VITAMIN D3 RECEPTOR IS A DELETION MUTANT. THE RESIDUES 165-211 WERE DELETED.

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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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9008 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.2 / Num. measured all: 28263
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.3 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1rk3

1rk3


Resolution: 2.5→40.36 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.854 / SU B: 11.654 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 1.311 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30939 434 4.8 %RANDOM
Rwork0.22919 ---
obs0.23282 8573 99.29 %-
all-9008 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 31 46 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9982761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31924.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86215369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.411511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021499
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21402
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.51280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9722001
X-RAY DIFFRACTIONr_scbond_it1.3933847
X-RAY DIFFRACTIONr_scangle_it2.284.5760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 35 -
Rwork0.268 605 -
obs--95.38 %

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