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- PDB-3vhu: Mineralocorticoid receptor ligand-binding domain with spironolactone -

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Basic information

Entry
Database: PDB / ID: 3vhu
TitleMineralocorticoid receptor ligand-binding domain with spironolactone
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION/INHIBITOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ACTIVATING MUTATION / HYPERTENSION / ANTAGONIST / SPIRONOLACTONE / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity ...nuclear steroid receptor activity / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity / sequence-specific double-stranded DNA binding / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / chromatin / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Retinoid X Receptor / Retinoid X 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 ...Retinoid X Receptor / Retinoid X 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
SPIRONOLACTONE / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSogabe, S. / Habuka, N.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Identification of Benzoxazin-3-one Derivatives as Novel, Potent, and Selective Nonsteroidal Mineralocorticoid Receptor Antagonists
Authors: Hasui, T. / Matsunaga, N. / Ora, T. / Ohyabu, N. / Nishigaki, N. / Imura, Y. / Igata, Y. / Matsui, H. / Motoyaji, T. / Tanaka, T. / Habuka, N. / Sogabe, S. / Ono, M. / Siedem, C.S. / Tang, T. ...Authors: Hasui, T. / Matsunaga, N. / Ora, T. / Ohyabu, N. / Nishigaki, N. / Imura, Y. / Igata, Y. / Matsui, H. / Motoyaji, T. / Tanaka, T. / Habuka, N. / Sogabe, S. / Ono, M. / Siedem, C.S. / Tang, T.P. / Gauthier, C. / De Meese, L.A. / Boyd, S.A. / Fukumoto, S.
History
DepositionSep 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Assembly

Deposited unit
A: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4232
Polymers34,0061
Non-polymers4171
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.526, 171.509, 42.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 34006.219 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, UNP residues 712-984 / Mutation: C808S, S810L
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-SNL / SPIRONOLACTONE / 17-HYDROXY-7ALPHA-MERCAPTO-3-OXO-17ALPHA-PREGN-4-ENE-21- CARBOXYLIC ACID / GAMMA-LACTONE ACETATE / Spironolactone


Mass: 416.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O4S / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 1.26M Lithium sulfate, 6% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 19, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 19366 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Rsym value: 0.059 / Net I/σ(I): 26.2
Reflection shellResolution: 2.11→2.2 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.515 / % possible all: 90.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AB2

2ab2


Resolution: 2.11→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.761 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24571 987 5.1 %RANDOM
Rwork0.19034 ---
obs0.19315 18299 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.646 Å2
Baniso -1Baniso -2Baniso -3
1-4.62 Å20 Å20 Å2
2---2.96 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.11→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 29 62 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222126
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9882887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8355249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68124.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26815385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.993158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211563
X-RAY DIFFRACTIONr_mcbond_it1.92321250
X-RAY DIFFRACTIONr_mcangle_it3.18532030
X-RAY DIFFRACTIONr_scbond_it5.2624876
X-RAY DIFFRACTIONr_scangle_it7.6826856
LS refinement shellResolution: 2.109→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 58 -
Rwork0.289 1104 -
obs--81.77 %
Refinement TLS params.Method: refined / Origin x: 24.6682 Å / Origin y: 21.9858 Å / Origin z: 3.0734 Å
111213212223313233
T0.1572 Å2-0.0008 Å20.0625 Å2-0.0279 Å2-0.0005 Å2--0.0546 Å2
L1.5109 °20.6821 °2-0.0194 °2-2.7998 °20.6876 °2--2.5934 °2
S0.0226 Å °-0.0456 Å °0.1754 Å °-0.2018 Å °0.0581 Å °0.0505 Å °-0.4091 Å °0.1776 Å °-0.0807 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A728 - 982
2X-RAY DIFFRACTION1A1001

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