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- PDB-5awk: Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl a... -

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Basic information

Entry
Database: PDB / ID: 5awk
TitleCrystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor,Vitamin D3 receptor
KeywordsTRANSCRIPTION / trandcription / Vitamin D / VDRE / RXR / co-factors / HORMONE
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors / G0 to G1 transition / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / core mediator complex / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / 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 / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / response to aldosterone / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / 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 / negative regulation of keratinocyte proliferation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / T-tubule / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / cellular response to epidermal growth factor stimulus / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / liver development / skeletal system development / apoptotic signaling pathway / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / animal organ morphogenesis / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / euchromatin / brain development / PPARA activates gene expression / Cytoprotection by HMOX1
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 / 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-YSE / 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 / Resolution: 2.9 Å
AuthorsAnami, Y. / Itoh, T. / Yamamoto, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity.
Authors: Anami, Y. / Sakamaki, Y. / Itoh, T. / Inaba, Y. / Nakabayashi, M. / Ikura, T. / Ito, N. / Yamamoto, K.
History
DepositionJul 4, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor,Vitamin D3 receptor
C: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5693
Polymers32,1662
Non-polymers4031
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-10 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.030, 41.970, 41.860
Angle α, β, γ (deg.)90.00, 95.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin D3 receptor,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: UNP RESIDUES 116-164, 212-423
Source method: isolated from a genetically manipulated source
Details: deletion mutant, residues 165-211 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 640-652 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-YSE / (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-ethyl-5-oxidanyl-pentan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol


Mass: 402.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H42O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→40.48 Å / Num. obs: 9246 / % possible obs: 75.2 % / Redundancy: 2 % / Net I/σ(I): 56

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata scaling
RefinementResolution: 2.9→40.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 49.299 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.596 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26653 207 4.6 %RANDOM
Rwork0.20817 ---
obs0.21074 4318 74.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.392 Å2
Baniso -1Baniso -2Baniso -3
1--6.08 Å2-0 Å2-1.28 Å2
2--6.24 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 29 8 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192076
X-RAY DIFFRACTIONr_bond_other_d00.022034
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9962810
X-RAY DIFFRACTIONr_angle_other_deg3.47134697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9375248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.79524.50591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4841511
X-RAY DIFFRACTIONr_chiral_restr0.0530.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212268
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7156.4491001
X-RAY DIFFRACTIONr_mcbond_other2.7156.4471000
X-RAY DIFFRACTIONr_mcangle_it4.619.6461246
X-RAY DIFFRACTIONr_mcangle_other4.6089.6481247
X-RAY DIFFRACTIONr_scbond_it2.7696.661075
X-RAY DIFFRACTIONr_scbond_other2.7686.6581076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6869.861565
X-RAY DIFFRACTIONr_long_range_B_refined7.31450.9912511
X-RAY DIFFRACTIONr_long_range_B_other7.31250.9872512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 19 -
Rwork0.316 341 -
obs--77.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7109-0.13440.0070.0655-0.05110.0736-0.0001-0.0261-0.0138-0.0164-0.00830.0142-0.0280.01180.00840.2531-0.0144-0.00080.2832-0.01340.276319.07920.372719.1431
22.93731.4336-0.51220.8313-0.67061.48710.10530.0691-0.07760.05-0.01980.02670.03690.1274-0.08560.24030.01390.00910.2882-0.03950.3035.9204-11.094611.0565
33.79343.41911.44968.9951-6.79611.65790.1342-0.0839-0.19510.14-0.2326-0.2508-0.06150.25310.09840.27910.01650.02180.2671-0.00580.322113.35594.622324.7574
40.1991-0.3006-0.53820.63891.17792.18160.01140.09130.10410.0082-0.0364-0.01130.0484-0.08960.0250.2197-0.05290.04060.0980.06360.35520.39453.503219.1831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 420
2X-RAY DIFFRACTION2C625 - 635
3X-RAY DIFFRACTION3A501
4X-RAY DIFFRACTION4A601 - 608

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