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- PDB-2ab2: Mineralocorticoid Receptor Double Mutant with Bound Spironolactone -

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Basic information

Entry
Database: PDB / ID: 2ab2
TitleMineralocorticoid Receptor Double Mutant with Bound Spironolactone
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION / Mineralocorticoid receptor / MR / Nuclear Receptor / Steroid Receptor / Spironolactone / Hypertension
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: 1.85 Å
AuthorsBledsoe, R.K. / Madauss, K.P. / Holt, J.A. / Apolito, C.J. / Lambert, M.H. / Pearce, K.H. / Stanley, T.B. / Stewart, E.L. / Trump, R.P. / Willson, T.M. / Williams, S.P.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A Ligand-mediated Hydrogen Bond Network Required for the Activation of the Mineralocorticoid Receptor
Authors: Bledsoe, R.K. / Madauss, K.P. / Holt, J.A. / Apolito, C.J. / Lambert, M.H. / Pearce, K.H. / Stanley, T.B. / Stewart, E.L. / Trump, R.P. / Willson, T.M. / Williams, S.P.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS A DIMER, BUT THE DIMER IN THE CRYSTAL IS IRRELEVANT BIOLOGICALLY. THE BIOLOGICAL DIMER IS CURRENTLY UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mineralocorticoid receptor
B: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2025
Polymers63,2732
Non-polymers9293
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.194, 89.939, 171.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer, but the non-crystallographic symmetry observed is biologically irrelevant

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Components

#1: Protein Mineralocorticoid receptor / / MR


Mass: 31636.598 Da / Num. of mol.: 2 / Fragment: MR Ligand Binding Domain / Mutation: C808S, S810L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Plasmid: pHis GST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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.: 2 / Source method: obtained synthetically / Formula: C24H32O4S / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 3, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Number: 54805 / Rmerge(I) obs: 0.063 / Χ2: 1.08 / D res high: 1.85 Å / D res low: 50 Å / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.995099.710.0260.9915.4
3.163.9999.110.0351.0644.5
2.763.1696.410.0541.0834.4
2.512.7694.710.0791.1154.6
2.332.5196.110.0951.0864.8
2.192.3397.610.1311.1185
2.082.1998.410.1581.085
1.992.0899.210.2221.0885.1
1.921.9999.510.3041.0764.7
1.851.9283.710.3951.1922.6
ReflectionResolution: 1.85→20 Å / Num. all: 56823 / Num. obs: 54805 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.08 / Net I/σ(I): 22.5
Reflection shellResolution: 1.85→1.92 Å / % possible obs: 83.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 4694 / Num. unique all: 4694 / Χ2: 1.192 / % possible all: 83.7

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Phasing

Phasing MRRfactor: 57.2 / Cor.coef. Fo:Fc: 21.8 / Cor.coef. Io to Ic: 27.1
Highest resolutionLowest resolution
Translation3.5 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR LBD

Resolution: 1.85→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3968 7 %Random
Rwork0.197 ---
all0.197 56872 --
obs0.197 54688 96.2 %-
Displacement parametersBiso mean: 20.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.018 Å20 Å20 Å2
2---0.024 Å20 Å2
3---0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 63 429 4596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.259
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5scd.par

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