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- PDB-4pf3: Mineralocorticoid receptor ligand-binding domain with compuond 37a -

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Basic information

Entry
Database: PDB / ID: 4pf3
TitleMineralocorticoid receptor ligand-binding domain with compuond 37a
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / HYPERTENSION / NON-STEROIDAL ANTAGONIST / ACTIVATING MUTATION / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / TBP-class protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / SUMOylation of intracellular receptors / positive regulation of non-canonical NF-kappaB signal transduction / Nuclear Receptor transcription pathway / nuclear receptor activity ...nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / TBP-class protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / SUMOylation of intracellular receptors / positive regulation of non-canonical NF-kappaB signal transduction / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / DNA-binding transcription factor activity / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / chromatin / signal transduction / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Retinoid X Receptor / Retinoid X 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 ...: / Retinoid X Receptor / Retinoid X 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-HFN / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSogabe, S. / Habuka, N.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Discovery of 6-[5-(4-fluorophenyl)-3-methyl-pyrazol-4-yl]-benzoxazin-3-one derivatives as novel selective nonsteroidal mineralocorticoid receptor antagonists
Authors: Hasui, T. / Ohyabu, N. / Ohra, T. / Fuji, K. / Sugimoto, T. / Fujimoto, J. / Asano, K. / Oosawa, M. / Shiotani, S. / Nishigaki, N. / Kusumoto, K. / Matsui, H. / Mizukami, A. / Habuka, N. / ...Authors: Hasui, T. / Ohyabu, N. / Ohra, T. / Fuji, K. / Sugimoto, T. / Fujimoto, J. / Asano, K. / Oosawa, M. / Shiotani, S. / Nishigaki, N. / Kusumoto, K. / Matsui, H. / Mizukami, A. / Habuka, N. / Sogabe, S. / Endo, S. / Ono, M. / Siedem, C.S. / Tang, T.P. / Gauthier, C. / De Meese, L.A. / Boyd, S.A. / Fukumoto, S.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,57910
Polymers31,6651
Non-polymers9149
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint23 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.050, 66.365, 74.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mineralocorticoid receptor / MR / Nuclear receptor subfamily 3 group C member 2


Mass: 31664.648 Da / Num. of mol.: 1 / Fragment: UNP residues 716-988 / Mutation: C808S, S810L, A976V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Production host: Escherichia coli (E. coli) / References: UniProt: P08235
#2: Chemical ChemComp-HFN / 6-[1-(2,2-difluoro-3-hydroxypropyl)-5-(4-fluorophenyl)-3-methyl-1H-pyrazol-4-yl]-2H-1,4-benzoxazin-3(4H)-one


Mass: 417.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F3N3O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM 3 FOUND IN P08235. (IDENTIFIRE: P08235-3)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH 8.0, 23% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.1→50 Å / Num. obs: 111992 / % possible obs: 95.1 % / Redundancy: 4.6 % / Rsym value: 0.052 / Net I/σ(I): 12.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / % possible all: 73.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFG

3wfg


Resolution: 1.1→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.843 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17683 5582 5 %RANDOM
Rwork0.15382 ---
obs0.15496 106388 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0 Å2
2---0.2 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 62 224 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9933046
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.915279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5224.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.714158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211668
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2951.8391027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6233.1231290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0262.3991215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.0319.6953692
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.06432242
X-RAY DIFFRACTIONr_sphericity_free32.148580
X-RAY DIFFRACTIONr_sphericity_bonded13.59952324
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 339 -
Rwork0.342 5767 -
obs--70.76 %

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