+Open data
-Basic information
Entry | Database: PDB / ID: 1hg4 | ||||||
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Title | Ultraspiracle ligand binding domain from Drosophila melanogaster | ||||||
Components | ULTRASPIRACLEEcdysone receptor | ||||||
Keywords | NUCLEAR HORMONE RECEPTOR / TRANSCRIPTION FACTOR / LIGAND BINDING | ||||||
Function / homology | Function and homology information ecdysone biosynthetic process / cellular response to ecdysone / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid / Transcriptional regulation of granulopoiesis / Cytoprotection by HMOX1 / ecdysone receptor holocomplex / activator ecdysone receptor complex ...ecdysone biosynthetic process / cellular response to ecdysone / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid / Transcriptional regulation of granulopoiesis / Cytoprotection by HMOX1 / ecdysone receptor holocomplex / activator ecdysone receptor complex / Recycling of bile acids and salts / Carnitine metabolism / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Nuclear Receptor transcription pathway / response to ecdysone / pupariation / ecdysone receptor-mediated signaling pathway / regulation of development, heterochronic / mushroom body development / metamorphosis / border follicle cell migration / polytene chromosome / hormone binding / regulation of organ growth / anatomical structure development / dendrite morphogenesis / nuclear steroid receptor activity / neuron remodeling / response to starvation / germ cell development / negative regulation of cell differentiation / core promoter sequence-specific DNA binding / nuclear receptor activity / cell differentiation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / signaling receptor binding / negative regulation of DNA-templated transcription / dendrite / lipid binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Schwabe, J.W.R. / Clayton, G.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: The Structure of the Ultraspiracle Ligand-Binding Domain Reveals a Nuclear Receptor Locked in an Inactive Conformation Authors: Clayton, G.M. / Peak-Chew, S.Y. / Evans, R.M. / Schwabe, J.W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hg4.cif.gz | 297.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hg4.ent.gz | 241.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/1hg4 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/1hg4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ereS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | BUT THE BIOLOGICALLY ACTIVE MOLECULE IS HETERODIMER |
-Components
#1: Protein | Mass: 31355.182 Da / Num. of mol.: 6 / Fragment: LIGAND-BINDING DOMAIN RESIDUES 230-508 Source method: isolated from a genetically manipulated source Details: PHOSPHATIDIC ACID MODELLED IN LIGAND BINDING POCKET OF 6 PROTEIN MONOMERS Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20153 #2: Chemical | ChemComp-LPP / #3: Water | ChemComp-HOH / | Compound details | THE C-TERMINAL STEROID-BINDING DOMAIN OF RECEPTOR FOR ECDYSONE. MAY PLAY AN IMPORTANT ROLE AS A ...THE C-TERMINAL STEROID-BINDING DOMAIN OF RECEPTOR FOR ECDYSONE. MAY PLAY AN IMPORTANT ROLE AS A MODULATOR IN INSECT METAMORPHO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.77 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 4.6 / Method: vapor diffusion / Details: used streak-seeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34 Å / Num. obs: 60384 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 4.4 |
Reflection | *PLUS Lowest resolution: 34 Å / % possible obs: 90 % / Num. measured all: 175324 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ERE Resolution: 2.4→34 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.4→34 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS |