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- PDB-5kct: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -
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Basic information
Entry | Database: PDB / ID: 5kct | |||||||||
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Title | Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an N-ethyl, 4-chlorobenzyl OBHS-N derivative | |||||||||
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![]() | TRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex | |||||||||
Function / homology | ![]() regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / 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 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / regulation of cellular response to insulin stimulus / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / negative regulation of miRNA transcription / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / RORA activates gene expression / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / Regulation of lipid metabolism by PPARalpha / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / PPARA activates gene expression / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / euchromatin / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / negative regulation of DNA-binding transcription factor activity / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / transcription coactivator binding / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / Circadian Clock / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / HATs acetylate histones / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Zhou, H.B. / Boonmuen, N. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, J. / Katzenellenbogen, B.S. / Griffin, P.R. / Katzenellenbogen, J.A. / Nettles, K.W. | |||||||||
![]() | ![]() Title: Full antagonism of the estrogen receptor without a prototypical ligand side chain. Authors: Srinivasan, S. / Nwachukwu, J.C. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Cavett, V. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, ...Authors: Srinivasan, S. / Nwachukwu, J.C. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Cavett, V. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, J. / Katzenellenbogen, B.S. / Griffin, P.R. / Katzenellenbogen, J.A. / Nettles, K.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.7 KB | Display | ![]() |
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PDB format | ![]() | 169.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kccC ![]() 5kcdC ![]() 5kceC ![]() 5kcfC ![]() 5kcuC ![]() 5kcwC ![]() 5kd9C C: citing same article ( |
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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: 29299.535 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) ![]() #3: Chemical | ChemComp-OB7 / ( | #4: Chemical | ChemComp-OB6 / ( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.61 % / Mosaicity: 0.529 ° |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 62319 / % possible obs: 96.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.062 / Χ2: 1.269 / Net I/av σ(I): 39.469 / Net I/σ(I): 8.9 / Num. measured all: 414995 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Resolution: 1.6→46.536 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.97 Å2 / Biso mean: 36.4823 Å2 / Biso min: 14.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→46.536 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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