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- PDB-1m2z: Crystal structure of a dimer complex of the human glucocorticoid ... -

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Basic information

Entry
Database: PDB / ID: 1m2z
TitleCrystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif
Components
  • glucocorticoid receptor
  • nuclear receptor coactivator 2
KeywordsHORMONE/HORMONE ACTIVATOR / glucocorticoid receptor / dexamethasone / TIF2 / dimer interface / Hormone binding pocket / charge clamp / coactivator / HORMONE-HORMONE ACTIVATOR COMPLEX
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / adrenal gland development / cellular response to steroid hormone stimulus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of gluconeogenesis / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cellular response to dexamethasone stimulus / regulation of cellular response to insulin stimulus / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / Recycling of bile acids and salts / cellular response to hormone stimulus / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / RORA activates gene expression / steroid binding / TBP-class protein binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / positive regulation of miRNA transcription / nuclear receptor coactivator activity / SUMOylation of intracellular receptors / synaptic transmission, glutamatergic / mRNA transcription by RNA polymerase II / response to progesterone / chromosome segregation / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Hsp90 protein binding / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / spindle / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / Circadian Clock / chromatin organization / HATs acetylate histones / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / chromatin binding / centrosome / synapse / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / protein kinase binding / apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II
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 / PAS domain / : / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 / 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEXAMETHASONE / Glucocorticoid receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Amore / Resolution: 2.5 Å
AuthorsBledsoe, R.B. / Montana, V.G. / Stanley, T.B. / Delves, C.J. / Apolito, C.J. / Mckee, D.D. / Consler, T.G. / Parks, D.J. / Stewart, E.L. / Willson, T.M. ...Bledsoe, R.B. / Montana, V.G. / Stanley, T.B. / Delves, C.J. / Apolito, C.J. / Mckee, D.D. / Consler, T.G. / Parks, D.J. / Stewart, E.L. / Willson, T.M. / Lambert, M.H. / Moore, J.T. / Pearce, K.H. / Xu, H.E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Reveals a Novel Mode of Receptor Dimerization and Coactivator Recognition
Authors: Bledsoe, R.B. / Montana, V.G. / Stanley, T.B. / Delves, C.J. / Apolito, C.J. / Mckee, D.D. / Consler, T.G. / Parks, D.J. / Stewart, E.L. / Willson, T.M. / Lambert, M.H. / Moore, J.T. / Pearce, K.H. / Xu, H.E.
History
DepositionJun 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
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
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 400COMPOUND THIS STRUCTURE CONTAINS: 1. A NOVEL LBD-LBD DIMER 2. A NOVEL CHARGE CLAMP FOR COACTIVATOR ...COMPOUND THIS STRUCTURE CONTAINS: 1. A NOVEL LBD-LBD DIMER 2. A NOVEL CHARGE CLAMP FOR COACTIVATOR RECOGNITION 3. A UNIQUE STEROID BINDING POCKET
Remark 600HETEROGEN THE ATOMS OF THE DETERGENT, BOG, B-OCTYLGLUCOSIDE, ARE ONLY PARTIALLY SEEN IN THE ...HETEROGEN THE ATOMS OF THE DETERGENT, BOG, B-OCTYLGLUCOSIDE, ARE ONLY PARTIALLY SEEN IN THE STRUCTURE. THE OCTANE CHAIN IS MISSING IN BOG 601. 6 ATOMS OF THE OCTANE CHAIN ARE MISSING IN BOG 701. THE O1 IS MISSING IN BOG 501.

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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
D: glucocorticoid receptor
E: nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1839
Polymers64,5214
Non-polymers1,6625
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.843, 125.843, 85.976
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein glucocorticoid receptor / GR


Mass: 29811.711 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain, residues 521-777 / Mutation: F602S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04150
#2: Protein/peptide nuclear receptor coactivator 2 / Transcriptional intermediary factor 2 / TIF2


Mass: 2448.833 Da / Num. of mol.: 2 / Fragment: TIF2 coactivator motif, residues 734-754 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The source of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q15596
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


Mass: 392.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29FO5 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: salts, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.3 mg/mlprotein1drop
250 mMHEPES1reservoirpH8.0
32.0 Mammonium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: MACSCIENCE / Detector: CCD / Date: Aug 15, 2002 / Details: Mar CCD 165 mm
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 27314 / Num. obs: 27095 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 35.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2727 / Rsym value: 0.718
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNX2000refinement
HKL-2000data reduction
RefinementMethod to determine structure: Amore
Starting model: GR model built on the PR structure

Resolution: 2.5→8 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1713 8 %RANDOM
Rwork0.237 ---
obs0.267 21317 81.8 %-
all-27314 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.2081 Å2 / ksol: 0.379381 e/Å3
Displacement parametersBiso mean: 67.2 Å2
Baniso -1Baniso -2Baniso -3
1--8.45 Å24.52 Å20 Å2
2---8.45 Å20 Å2
3---16.9 Å2
Refine analyzeLuzzati coordinate error free: 0.42 Å / Luzzati sigma a free: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 102 205 4783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.231.5
X-RAY DIFFRACTIONc_mcangle_it3.932
X-RAY DIFFRACTIONc_scbond_it5.412
X-RAY DIFFRACTIONc_scangle_it6.622.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 168 7.9 %
Rwork0.292 1958 -
obs--49.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3LOCALPARM.XPL
X-RAY DIFFRACTION4BSXPI3_BOND.XPL
X-RAY DIFFRACTION5X.XPRM
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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