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Yorodumi- PDB-1q4x: Crystal Structure of Human Thyroid Hormone Receptor beta LBD in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q4x | ||||||
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Title | Crystal Structure of Human Thyroid Hormone Receptor beta LBD in complex with specific agonist GC-24 | ||||||
Components | Thyroid hormone receptor beta-1 | ||||||
Keywords | TRANSCRIPTION / conformational change in two framework helices upon ligand binding | ||||||
Function / homology | Function and homology information retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / retinoic acid receptor signaling pathway / sensory perception of sound / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / transcription coactivator binding / chromatin DNA binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Borngraeber, S. / Budny, M.J. / Chiellini, G. / Cunha-Lima, S.T. / Togashi, M. / Webb, P. / Baxter, J.D. / Scanlan, T.S. / Fletterick, R.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Ligand selectivity by seeking hydrophobicity in thyroid hormone receptor. Authors: Borngraeber, S. / Budny, M.J. / Chiellini, G. / Cunha-Lima, S.T. / Togashi, M. / Webb, P. / Baxter, J.D. / Scanlan, T.S. / Fletterick, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q4x.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q4x.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 1q4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q4x ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q4x | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28582.080 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THRB OR NR1A2 OR ERBA2 OR THR1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P10828 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: PEG 3350, sodium acetate, glucose, cymal-2, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
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: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2002 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→24.47 Å / Num. all: 10076 / Num. obs: 9368 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Biso Wilson estimate: 59.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.8→2.98 Å / % possible all: 81.5 |
Reflection | *PLUS % possible obs: 93 % / Num. measured all: 113019 |
Reflection shell | *PLUS % possible obs: 81.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Human Thyroid Hormone Receptor beta in complex with agonist GC-1; the crystal structure was solved in our lab, but not deposited at the PDB Resolution: 2.8→24.47 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 60.08 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→24.47 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.98 Å |