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- PDB-2oax: Crystal structure of the S810L mutant mineralocorticoid receptor ... -

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Basic information

Entry
Database: PDB / ID: 2oax
TitleCrystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION / ALDOSTERONE / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ACTIVATING MUTATION / HYPERTENSION / ANTAGONIST / SPIRONOLACTONE
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / 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 / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / 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
SPIRONOLACTONE / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHuyet, J. / Pinon, G.M. / Fay, M.R. / Rafestin-Oblin, M.E. / Fagart, J.
CitationJournal: Mol.Pharmacol. / Year: 2007
Title: Structural basis of spirolactone recognition by the mineralocorticoid receptor
Authors: Huyet, J. / Pinon, G.M. / Fay, M.R. / Fagart, J. / Rafestin-Oblin, M.E.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Mineralocorticoid receptor
D: Mineralocorticoid receptor
E: Mineralocorticoid receptor
F: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,70812
Polymers178,2086
Non-polymers2,4996
Water6,107339
1
A: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1182
Polymers29,7011
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1182
Polymers29,7011
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1182
Polymers29,7011
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1182
Polymers29,7011
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1182
Polymers29,7011
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1182
Polymers29,7011
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.198, 122.198, 91.808
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Mineralocorticoid receptor / MR


Mass: 29701.410 Da / Num. of mol.: 6 / Fragment: LIGAND-BINDING DOMAIN / Mutation: S810L,C910A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: EXPRESSED AS GST FUSION / Gene: NR3C2, MCR, MLR / Plasmid: PGEX PMRLBDL810 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) RIL / References: UniProt: P08235
#2: Chemical
ChemComp-SNL / SPIRONOLACTONE / 17-HYDROXY-7ALPHA-MERCAPTO-3-OXO-17ALPHA-PREGN-4-ENE-21- CARBOXYLIC ACID / GAMMA-LACTONE ACETATE


Mass: 416.573 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H32O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 81 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979707 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2005 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979707 Å / Relative weight: 1
ReflectionResolution: 2.29→14.92 Å / Num. all: 69379 / Num. obs: 63172 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.119 / Net I/σ(I): 13
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 5.65 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.66 / Num. unique all: 10661 / Rsym value: 0.945 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Xnemodata collection
PHASERphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: monomere A from PDB 1Y9R

1y9r


Resolution: 2.29→14.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 258409.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3220 5.1 %RANDOM
Rwork0.24 ---
obs0.24 62950 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4877 Å2 / ksol: 0.331702 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å23.33 Å20 Å2
2---1.14 Å20 Å2
3---2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.29→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11503 0 174 339 12016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.412.5
LS refinement shellResolution: 2.29→2.43 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 589 5.3 %
Rwork0.334 10506 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2SNL.paramSNL.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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