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- PDB-3mne: Crystal structure of the agonist form of mouse glucocorticoid rec... -

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Basic information

Entry
Database: PDB / ID: 3mne
TitleCrystal structure of the agonist form of mouse glucocorticoid receptor stabilized by F608S mutation at 1.96A
Components
  • Glucocorticoid receptor
  • Nuclear receptor coactivator 2 peptide
KeywordsHORMONE RECEPTOR / protein-ligand complex / steroid nuclear receptor / mouse / agonist / co-activator
Function / homology
Function and homology information


Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Endogenous sterols ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Endogenous sterols / HATs acetylate histones / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / response to cortisol / steroid hormone binding / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / glucocorticoid metabolic process / neuroinflammatory response / Estrogen-dependent gene expression / mammary gland duct morphogenesis / microglia differentiation / astrocyte differentiation / maternal behavior / motor behavior / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of gluconeogenesis / adrenal gland development / locomotor rhythm / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / positive regulation of adipose tissue development / steroid binding / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / cellular response to dexamethasone stimulus / response to progesterone / nuclear receptor binding / synaptic transmission, glutamatergic / promoter-specific chromatin binding / Hsp90 protein binding / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / positive regulation of miRNA transcription / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / RNA polymerase II transcription regulator complex / nuclear receptor activity / circadian rhythm / positive regulation of neuron apoptotic process / chromatin organization / chromosome / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / nuclear speck / nuclear body / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / negative regulation of DNA-templated transcription / synapse / centrosome / chromatin binding / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone 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
DEXAMETHASONE / Glucocorticoid receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSchoch, G.A. / Seitz, T. / Benz, J. / Banner, D. / Stihle, M. / D'Arcy, B. / Thoma, R. / Sterner, R. / Hennig, M. / Ruf, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening.
Authors: Seitz, T. / Thoma, R. / Schoch, G.A. / Stihle, M. / Benz, J. / D'Arcy, B. / Wiget, A. / Ruf, A. / Hennig, M. / Sterner, R.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Glucocorticoid receptor
B: Nuclear receptor coactivator 2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2675
Polymers31,6902
Non-polymers5773
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-10 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.820, 71.820, 128.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 30096.092 Da / Num. of mol.: 1 / Fragment: UNP residues 527-783 / Mutation: F608S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr3c1, Grl, Grl1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06537
#2: Protein/peptide Nuclear receptor coactivator 2 peptide / NCoA-2 / Transcriptional intermediary factor 2 / Glucocorticoid receptor-interacting protein 1 / GRIP-1


Mass: 1593.844 Da / Num. of mol.: 1 / Fragment: TIF2 coactivator motif, residues 740-752 / Source method: obtained synthetically
Details: The sequence occurs naturally in Mus musculus (mouse)
References: UniProt: Q61026
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


Mass: 392.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29FO5 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: 0.5 M ammonium sulfate, 0.9 M sodium tartrate, 0.1 M PIPES pH 7.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å
DetectorDate: Jul 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.96→12.9 Å / Num. all: 26835 / Num. obs: 26835 / % possible obs: 99.7 % / Redundancy: 11.22 % / Biso Wilson estimate: 26.87 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.72
Reflection shellResolution: 1.96→2.06 Å / Redundancy: 9.18 % / Mean I/σ(I) obs: 2.41 / Num. unique all: 3555 / Rsym value: 0.4566

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER-TNT2.5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M2Z

1m2z


Resolution: 1.96→12.98 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 1335 5 %RANDOM
Rwork0.151 ---
obs0.1527 26682 99.54 %-
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.04074819 Å20 Å20 Å2
2---4.04074819 Å20 Å2
3---8.08149639 Å2
Refine analyzeLuzzati coordinate error obs: 0.1776 Å
Refinement stepCycle: LAST / Resolution: 1.96→12.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 40 286 2441
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01122572
X-RAY DIFFRACTIONt_angle_deg1.05330542
X-RAY DIFFRACTIONt_dihedral_angle_d19.934540
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01532
X-RAY DIFFRACTIONt_gen_planes0.0143215
X-RAY DIFFRACTIONt_it1.634225720
X-RAY DIFFRACTIONt_nbd0.036475
LS refinement shellResolution: 1.96→2.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.245 188 4.47 %
Rwork0.2108 4022 -
all0.2123 4210 -
obs--99.54 %

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