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

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Basic information

Entry
Database: PDB / ID: 3mno
TitleCrystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, F608S) mutations at 1.55A
Components
  • Glucocorticoid receptor
  • Nuclear receptor coactivator 2 peptide
KeywordsHORMONE RECEPTOR / protein-ligand complex / steroid nuclear receptor / mouse GR / 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 / Regulation of lipid metabolism by PPARalpha / steroid hormone binding / Cytoprotection by HMOX1 / glucocorticoid metabolic process / response to cortisol / neuroinflammatory response / Estrogen-dependent gene expression / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / adrenal gland development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of gluconeogenesis / locomotor rhythm / motor behavior / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / cellular response to dexamethasone stimulus / cellular response to transforming growth factor beta stimulus / core promoter sequence-specific DNA binding / transcription regulator inhibitor activity / steroid binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / response to progesterone / TBP-class protein binding / nuclear receptor binding / negative regulation of smoothened signaling pathway / synaptic transmission, glutamatergic / promoter-specific chromatin binding / Hsp90 protein binding / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / circadian rhythm / response to wounding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / spindle / nuclear receptor activity / positive regulation of neuron apoptotic process / chromosome / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / protein dimerization activity / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / protein domain specific 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 / cytoplasm / cytosol
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 / THIOCYANATE ION / Glucocorticoid receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 22, 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)32,4117
Polymers31,7182
Non-polymers6935
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-13 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.405, 71.405, 127.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 30124.143 Da / Num. of mol.: 1 / Fragment: UNP residues 527-783 / Mutation: A611V, 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

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Non-polymers , 4 types, 370 molecules

#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
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium thiocyanate, 0.1 M Bis-Tris pH 6.5, 0.7 M lithium sulfate, 10 % Glycerol, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorDate: Nov 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→35.7 Å / Num. all: 53304 / Num. obs: 53304 / % possible obs: 99.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 23.767 Å2 / Rsym value: 0.067 / Net I/σ(I): 21.7
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7760 / Rsym value: 0.846 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER-TNT2.5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MNE

3mne


Resolution: 1.55→35.69 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 2697 5.07 %RANDOM
Rwork0.1654 ---
obs0.1665 53239 99.52 %-
Displacement parametersBiso mean: 30.65 Å2
Baniso -1Baniso -2Baniso -3
1--4.47056127 Å20 Å20 Å2
2---4.47056127 Å20 Å2
3---8.94112254 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 46 365 2543
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01123312
X-RAY DIFFRACTIONt_angle_deg1.1831622
X-RAY DIFFRACTIONt_dihedral_angle_d15.984740
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012542
X-RAY DIFFRACTIONt_gen_planes0.0163355
X-RAY DIFFRACTIONt_it1.694233120
X-RAY DIFFRACTIONt_nbd0.192285
LS refinement shellResolution: 1.55→1.64 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2103 419 4.91 %
Rwork0.2109 8122 -
all0.2109 8541 -
obs--99.52 %

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