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- PDB-1m2z: Crystal structure of a dimer complex of the human glucocorticoid ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m2z | ||||||
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Title | Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif | ||||||
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![]() | HORMONE/HORMONE ACTIVATOR / glucocorticoid receptor / dexamethasone / TIF2 / dimer interface / Hormone binding pocket / charge clamp / coactivator / HORMONE-HORMONE ACTIVATOR COMPLEX | ||||||
Function / homology | ![]() 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 / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / regulation of cellular response to insulin stimulus / 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 / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / steroid binding / Regulation of lipid metabolism by PPARalpha / cellular response to dexamethasone stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / synaptic transmission, glutamatergic / chromosome segregation / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Hsp90 protein binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / spindle / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / Circadian Clock / chromatin organization / HATs acetylate histones / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Potential therapeutics for SARS / transcription coactivator activity / nuclear body / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / cell division / negative regulation of DNA-templated transcription / centrosome / apoptotic process / synapse / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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. ...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. | ||||||
![]() | ![]() 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 |
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Remark 400 | COMPOUND 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 600 | HETEROGEN 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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() ![]() #2: Protein/peptide | 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 | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.6 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MACSCIENCE / Detector: CCD / Date: Aug 15, 2002 / Details: Mar CCD 165 mm |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.2081 Å2 / ksol: 0.379381 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.42 Å / Luzzati sigma a free: 0.4 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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